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- PDB-3lk4: Crystal structure of CapZ bound to the uncapping motif from CD2AP -

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基本情報

登録情報
データベース: PDB / ID: 3lk4
タイトルCrystal structure of CapZ bound to the uncapping motif from CD2AP
要素
  • CD2-associated protein
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1 and 2
キーワードPROTEIN BINDING / CapZ / CD2AP / actin filaments / uncapping / actin-filament regulators / protein-protein comple / Actin capping / Actin-binding / Cytoplasm / Cytoskeleton
機能・相同性
機能・相同性情報


Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / response to glial cell derived neurotrophic factor / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / transforming growth factor beta1 production / negative regulation of small GTPase mediated signal transduction ...Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / response to glial cell derived neurotrophic factor / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / transforming growth factor beta1 production / negative regulation of small GTPase mediated signal transduction / localization of cell / negative regulation of filopodium assembly / slit diaphragm / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / F-actin capping protein complex / WASH complex / sperm head-tail coupling apparatus / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / protein heterooligomerization / collateral sprouting / renal albumin absorption / substrate-dependent cell migration, cell extension / phosphatidylinositol 3-kinase regulatory subunit binding / cell-cell adhesion mediated by cadherin / barbed-end actin filament capping / cell junction assembly / filopodium assembly / membrane organization / actin polymerization or depolymerization / regulation of lamellipodium assembly / cell-cell junction organization / regulation of cell morphogenesis / Nephrin family interactions / podosome / lamellipodium assembly / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / cortical cytoskeleton / neurotrophin TRK receptor signaling pathway / D-glucose import / cell leading edge / filamentous actin / brush border / protein secretion / adipose tissue development / lymph node development / stress-activated MAPK cascade / ruffle / ERK1 and ERK2 cascade / actin filament polymerization / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / actin filament organization / liver development / trans-Golgi network membrane / positive regulation of protein secretion / regulation of actin cytoskeleton organization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein catabolic process / synapse organization / response to insulin / cell morphogenesis / neuromuscular junction / regulation of synaptic plasticity / structural constituent of cytoskeleton / SH3 domain binding / lipid metabolic process / response to wounding / response to virus / centriolar satellite / Schaffer collateral - CA1 synapse / positive regulation of protein localization to nucleus / Z disc / fibrillar center / male gonad development / actin filament binding / late endosome / cell migration / actin cytoskeleton / lamellipodium / T cell receptor signaling pathway / actin cytoskeleton organization / growth cone / protein-containing complex assembly / vesicle / response to oxidative stress / negative regulation of neuron apoptotic process / cell population proliferation / postsynaptic density / cadherin binding / inflammatory response / axon / cell division / apoptotic process
類似検索 - 分子機能
F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit ...F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / : / Ribosomal protein S3 C-terminal domain / Variant SH3 domain / Aspartate Aminotransferase, domain 1 / SH3 domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / CD2-associated protein
類似検索 - 構成要素
生物種Gallus gallus (ニワトリ)
homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.99 Å
データ登録者Hernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / Cooper, J.A. / Robinson, R.C.
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2010
タイトル: Structural characterization of a capping protein interaction motif defines a family of actin filament regulators.
著者: Hernandez-Valladares, M. / Kim, T. / Kannan, B. / Tung, A. / Aguda, A.H. / Larsson, M. / Cooper, J.A. / Robinson, R.C.
履歴
登録2010年1月27日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02010年4月7日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22019年12月18日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.32023年11月1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

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集合体

登録構造単位
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
C: CD2-associated protein
D: F-actin-capping protein subunit alpha-1
E: F-actin-capping protein subunit beta isoforms 1 and 2
F: CD2-associated protein
G: F-actin-capping protein subunit alpha-1
H: F-actin-capping protein subunit beta isoforms 1 and 2
I: CD2-associated protein
J: F-actin-capping protein subunit alpha-1
K: F-actin-capping protein subunit beta isoforms 1 and 2
L: CD2-associated protein
M: F-actin-capping protein subunit alpha-1
N: F-actin-capping protein subunit beta isoforms 1 and 2
O: CD2-associated protein
P: F-actin-capping protein subunit alpha-1
Q: F-actin-capping protein subunit beta isoforms 1 and 2
R: CD2-associated protein
S: F-actin-capping protein subunit alpha-1
T: F-actin-capping protein subunit beta isoforms 1 and 2
U: CD2-associated protein
V: F-actin-capping protein subunit alpha-1
W: F-actin-capping protein subunit beta isoforms 1 and 2
X: CD2-associated protein
Y: F-actin-capping protein subunit alpha-1
Z: F-actin-capping protein subunit beta isoforms 1 and 2
0: CD2-associated protein
1: F-actin-capping protein subunit alpha-1
2: F-actin-capping protein subunit beta isoforms 1 and 2
3: CD2-associated protein
4: F-actin-capping protein subunit alpha-1
5: F-actin-capping protein subunit beta isoforms 1 and 2
6: CD2-associated protein
7: F-actin-capping protein subunit alpha-1
8: F-actin-capping protein subunit beta isoforms 1 and 2
9: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)811,55936
ポリマ－811,55936
非ポリマー00
水52,2442900
1
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
C: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-55 kcal/mol
Surface area23070 Å2
手法PISA
2
D: F-actin-capping protein subunit alpha-1
E: F-actin-capping protein subunit beta isoforms 1 and 2
F: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-56 kcal/mol
Surface area23020 Å2
手法PISA
3
G: F-actin-capping protein subunit alpha-1
H: F-actin-capping protein subunit beta isoforms 1 and 2
I: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-56 kcal/mol
Surface area23130 Å2
手法PISA
4
J: F-actin-capping protein subunit alpha-1
K: F-actin-capping protein subunit beta isoforms 1 and 2
L: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-55 kcal/mol
Surface area23040 Å2
手法PISA
5
M: F-actin-capping protein subunit alpha-1
N: F-actin-capping protein subunit beta isoforms 1 and 2
O: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-56 kcal/mol
Surface area23110 Å2
手法PISA
6
P: F-actin-capping protein subunit alpha-1
Q: F-actin-capping protein subunit beta isoforms 1 and 2
R: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-55 kcal/mol
Surface area23090 Å2
手法PISA
7
S: F-actin-capping protein subunit alpha-1
T: F-actin-capping protein subunit beta isoforms 1 and 2
U: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-55 kcal/mol
Surface area23000 Å2
手法PISA
8
V: F-actin-capping protein subunit alpha-1
W: F-actin-capping protein subunit beta isoforms 1 and 2
X: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-55 kcal/mol
Surface area23120 Å2
手法PISA
9
Y: F-actin-capping protein subunit alpha-1
Z: F-actin-capping protein subunit beta isoforms 1 and 2
0: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-56 kcal/mol
Surface area23160 Å2
手法PISA
10
1: F-actin-capping protein subunit alpha-1
2: F-actin-capping protein subunit beta isoforms 1 and 2
3: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-56 kcal/mol
Surface area23080 Å2
手法PISA
11
4: F-actin-capping protein subunit alpha-1
5: F-actin-capping protein subunit beta isoforms 1 and 2
6: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-56 kcal/mol
Surface area23010 Å2
手法PISA
12
7: F-actin-capping protein subunit alpha-1
8: F-actin-capping protein subunit beta isoforms 1 and 2
9: CD2-associated protein


分子量 (理論値)分子数
合計 (水以外)67,6303
ポリマ－67,6303
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-54 kcal/mol
Surface area23120 Å2
手法PISA
単位格子
Length a, b, c (Å)59.728, 142.341, 192.999
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
73
83
93
103
113
123

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 8:276
211chain D and resid 8:276
311chain G and resid 8:276
411chain J and resid 8:276
511chain M and resid 8:276
611chain P and resid 8:276
711chain S and resid 8:276
811chain V and resid 8:276
911chain Y and resid 8:276
1011chain 1 and resid 8:276
1111chain 4 and resid 8:276
1211chain 7 and resid 8:276
112chain B and resid 4:244
212chain E and resid 4:244
312chain H and resid 4:244
412chain K and resid 4:244
512chain N and resid 4:244
612chain Q and resid 4:244
712chain T and resid 4:244
812chain W and resid 4:244
912chain Z and resid 4:244
1012chain 2 and resid 4:244
1112chain 5 and resid 4:244
1212chain 8 and resid 4:244
113chain C and resid 475:503
213chain F and resid 475:503
313chain I and resid 475:503
413chain L and resid 475:503
513chain O and resid 475:503
613chain R and resid 475:503
713chain U and resid 475:503
813chain X and resid 475:503
913chain 0 and resid 475:503
1013chain 3 and resid 475:503
1113chain 6 and resid 475:503
1213chain 9 and resid 475:503

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
F-actin-capping protein subunit alpha-1 / CapZ 36/32 / Beta-actinin subunit I


分子量: 33001.789 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Gallus gallus (ニワトリ) / 遺伝子: CAPZA1 / プラスミド: pET3d / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 Star (DE3) / 参照: UniProt: P13127
#2: タンパク質
F-actin-capping protein subunit beta isoforms 1 and 2 / CapZ B1 and B2 / CapZ 36/32 / Beta-actinin subunit II


分子量: 31403.449 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Gallus gallus (ニワトリ) / 遺伝子: CAPZA1, CAPZB / プラスミド: pET3d / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 Star (DE3) / 参照: UniProt: P14315
#3: タンパク質・ペプチド
CD2-associated protein / Cas ligand with multiple SH3 domains / Adapter protein CMS


分子量: 3224.673 Da / 分子数: 12 / 由来タイプ: 合成 / 詳細: peptide synthesis / 由来: (合成) homo sapiens (ヒト) / 参照: UniProt: Q9Y5K6
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2900 / 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: 2.02 Å3/Da / 溶媒含有率: 39.16 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 30% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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データ収集

回折平均測定温度: 105 K
放射光源由来: シンクロトロン / サイト: NSRRC / ビームライン: BL13B1
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年11月14日 / 詳細: phosphor screen, fiber-optic taper, CCD chip
放射モノクロメーター: double-crystal / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長相対比: 1
反射解像度: 1.99→20 Å / Num. obs: 358158 / % possible obs: 82.6 % / 冗長度: 3.2 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 24.7
反射 シェル解像度: 2→2.1 Å / 冗長度: 3.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.3 / Num. unique all: 16631 / Rsym value: 0.418 / % possible all: 76.8

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
MOLREP位相決定
PHENIX(phenix.refine: 1.5_2)精密化
HKL-2000データ削減
HKL-2000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: 3LK2

3lk2


解像度: 1.99→19.984 Å / SU ML: 0.3 / Isotropic thermal model: RANDOM / 交差検証法: THROUGHOUT / σ(F): 1.96 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2722 18001 5.03 %
Rwork0.2253 --
obs0.2277 358158 82.25 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 45.913 Å2 / ksol: 0.32 e/Å3
原子変位パラメータBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.1232 Å20.3329 Å2-0.8627 Å2
2--2.3544 Å2-0.7957 Å2
3----4.8098 Å2
精密化ステップサイクル: LAST / 解像度: 1.99→19.984 Å
タンパク質核酸リガンド溶媒全体
原子数51470 0 0 2900 54370
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00752442
X-RAY DIFFRACTIONf_angle_d1.0270986
X-RAY DIFFRACTIONf_dihedral_angle_d19.01219408
X-RAY DIFFRACTIONf_chiral_restr0.0737743
X-RAY DIFFRACTIONf_plane_restr0.0049325
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A2185X-RAY DIFFRACTIONPOSITIONAL
12D2185X-RAY DIFFRACTIONPOSITIONAL0.033
13G2185X-RAY DIFFRACTIONPOSITIONAL0.041
14J2185X-RAY DIFFRACTIONPOSITIONAL0.036
15M2185X-RAY DIFFRACTIONPOSITIONAL0.043
16P2185X-RAY DIFFRACTIONPOSITIONAL0.026
17S2185X-RAY DIFFRACTIONPOSITIONAL0.038
18V2185X-RAY DIFFRACTIONPOSITIONAL0.043
19Y2185X-RAY DIFFRACTIONPOSITIONAL0.022
11012185X-RAY DIFFRACTIONPOSITIONAL0.022
11142185X-RAY DIFFRACTIONPOSITIONAL0.037
11272185X-RAY DIFFRACTIONPOSITIONAL0.042
21B1864X-RAY DIFFRACTIONPOSITIONAL
22E1864X-RAY DIFFRACTIONPOSITIONAL0.032
23H1864X-RAY DIFFRACTIONPOSITIONAL0.049
24K1864X-RAY DIFFRACTIONPOSITIONAL0.035
25N1864X-RAY DIFFRACTIONPOSITIONAL0.05
26Q1864X-RAY DIFFRACTIONPOSITIONAL0.024
27T1864X-RAY DIFFRACTIONPOSITIONAL0.033
28W1864X-RAY DIFFRACTIONPOSITIONAL0.05
29Z1864X-RAY DIFFRACTIONPOSITIONAL0.024
21021864X-RAY DIFFRACTIONPOSITIONAL0.024
21151864X-RAY DIFFRACTIONPOSITIONAL0.034
21281864X-RAY DIFFRACTIONPOSITIONAL0.049
31C225X-RAY DIFFRACTIONPOSITIONAL
32F225X-RAY DIFFRACTIONPOSITIONAL0.022
33I225X-RAY DIFFRACTIONPOSITIONAL0.03
34L225X-RAY DIFFRACTIONPOSITIONAL0.023
35O225X-RAY DIFFRACTIONPOSITIONAL0.028
36R225X-RAY DIFFRACTIONPOSITIONAL0.015
37U225X-RAY DIFFRACTIONPOSITIONAL0.022
38X225X-RAY DIFFRACTIONPOSITIONAL0.029
390225X-RAY DIFFRACTIONPOSITIONAL0.017
3103225X-RAY DIFFRACTIONPOSITIONAL0.013
3116225X-RAY DIFFRACTIONPOSITIONAL0.024
3129225X-RAY DIFFRACTIONPOSITIONAL0.029
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9902-2.06120.33516090.2833116475
2.0612-2.14370.322216600.26593145476
2.1437-2.24110.330616370.27273154076
2.2411-2.35910.316617630.25923200478
2.3591-2.50660.316217670.2523356081
2.5066-2.69970.304118620.24553502885
2.6997-2.97060.2919720.24163661989
2.9706-3.39870.287919380.23593702590
3.3987-4.27510.237418550.20063551686
4.2751-19.98480.206119380.17353624788
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)
10.3788-0.22080.40872.4473-0.51230.6558-0.01710.1497-0.19280.60650.13430.1288-0.0439-0.41070.0485-0.0870.0432-0.00390.22960.04290.1709-13.247599.5705107.3952
21.19231.4572-0.53143.28790.34480.6249-0.77530.303-0.8872-1.94840.0334-0.25330.1728-0.8729-1.0063-0.04960.2032-0.91720.4763-0.0553-0.5308-21.770787.625386.2054
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890.61330.02141.18440.01890.0592.3042-0.4561-0.2514-0.6458-0.62850.0424-0.75640.34230.26870.29630.9147-0.12310.14380.39910.22480.94411.384921.9099-76.9884
900.170.1818-0.38390.7101-0.32990.9412-0.5735-0.00650.0241-0.57840.8275-0.1272-0.22960.7283-0.17680.8964-0.1898-0.16780.3613-0.02340.2119-14.370723.3403-89.5437
910.55390.2392-0.47371.4133-0.2161.4279-0.00750.09250.0950.51520.228-0.0221-0.39280.2301-0.18890.28350.02390.04110.175-0.03430.158429.4375-28.599510.9055
921.00070.75570.64951.5611-0.49271.0779-0.06720.19750.0121-0.9986-0.2405-0.61090.53930.8630.15470.64530.20220.39220.50880.1370.282437.9604-16.6626-10.2869
931.96870.21370.02982.3831-1.25710.7647-0.10610.43830.0135-0.92550.0116-0.17660.47570.05240.11550.73070.00330.18160.15270.00830.12221.3507-13.3872-12.2987
940.938-0.87780.72292.81460.13050.7546-0.57520.0136-0.28450.56550.20510.82820.2085-0.15070.12540.40030.12070.17690.25920.12270.389-7.8192-7.362714.4656
952.1163-0.7511-0.07851.2010.28640.0439-0.2655-0.4558-0.09210.6730.13180.20050.0691-0.33630.11910.47530.04260.10410.2134-0.00570.186220.1014-22.546814.2738
961.33920.4924-0.33492.3379-0.27470.3209-0.7221-0.4317-0.62780.76040.53770.7380.1604-0.06280.16590.62980.19550.39520.32820.21120.46582.1571-31.432722.3899
971.2574-0.0829-1.06373.8288-0.85082.0724-0.5411-0.3211-0.15510.63020.24580.65480.75820.07910.3020.41390.1570.29930.16540.11490.3261-4.6939-19.165122.2957
983.1593-0.3643-0.81343.2805-0.5090.7089-0.3162-0.3919-0.0030.29590.19460.1873-0.090.16360.06180.34610.1150.12350.18230.03280.18714.392-11.533715.8806
992.17760.278-1.18071.0714-0.92341.2244-0.50010.2330.97260.71870.52880.1239-0.19980.0699-0.0850.63660.2238-0.09510.47260.20141.007141.3213-22.222912.3091
1000.1767-0.2507-0.0961.0622-0.27810.3342-0.5807-0.2482-0.13240.89550.6237-0.2030.17320.5888-0.13020.78840.22460.20920.39860.04220.249315.5827-23.566124.9095
1010.53650.364-0.06490.1898-0.02380.1647-0.01440.0713-0.07030.05520.0795-0.05720.51190.1718-0.05120.82150.13560.08510.38150.01390.227829.4966-28.5147-53.3602
1021.6997-0.3273-0.68510.71320.15661.3187-0.1411-0.35390.0227-0.11060.1048-0.00450.36120.43030.06650.47790.04680.15350.2498-0.01130.124938.1988-16.561-74.4602
1031.89940.8428-0.52542.1531-0.41050.1929-0.21770.2664-0.0182-0.44820.2670.06750.1321-0.1645-0.00840.6627-0.07110.08250.1806-0.02090.114421.601-13.3599-76.6399
1041.02290.9851-0.62531.8837-1.39841.19650.25390.48170.51720.29760.2180.4234-0.42-0.2807-0.41770.52240.10880.09020.14040.11270.272-7.8788-7.4191-50.1786
1050.3563-0.3149-0.64290.91820.30251.29470.1031-0.1201-0.00830.6632-0.18760.20180.37720.19140.06890.8340.03860.12480.2149-0.02560.226120.0215-22.5418-50.1169
1061.14870.9667-0.45810.7323-0.32490.4809-0.2588-0.0476-0.3046-0.34420.095-0.03390.22320.22530.14090.57490.10660.13720.17090.07360.20282.0477-31.5154-42.2036
1070.8710.3857-0.15721.6276-1.25410.9534-0.24040.02230.0747-0.05770.12670.14620.16140.12330.08460.44170.09030.1240.07690.04830.1909-4.8264-19.2522-42.2948
1081.96470.0883-0.63671.2617-0.09630.8921-0.0457-0.0030.1227-0.06710.12060.0782-0.41660.1094-0.11230.53470.06040.10570.09350.0220.15934.2943-11.5692-48.5839
1094.09862.0122-0.32674.07010.0737.80810.62860.62060.27550.2270.5060.37190.11270.8838-0.69860.90860.2107-0.050.5810.00930.468141.2634-22.1024-51.8491
1100.1512-0.0640.04870.30760.35560.7473-0.2518-0.14620.0452-0.20530.33080.03910.31640.72560.01040.61020.0430.16990.3391-0.02380.195815.4091-23.6617-39.515
1110.41520.5051-0.10640.7394-0.00320.5060.0189-0.01960.0506-0.10070.0012-0.24260.03330.28870.05520.02590.0450.00020.207-0.02020.173128.0886-28.509875.0663
1120.73070.38230.85880.663-0.79893.6879-0.00980.24330.1335-0.2744-0.2045-0.38450.39011.29330.39240.08370.09990.10360.60950.06050.207236.6333-16.536453.8769
1130.94430.06020.12010.6204-1.50262.549-0.01410.14950.1131-0.1083-0.047-0.01950.15030.2170.06250.09060.03860.05580.18530.01230.161520.0187-13.322751.8251
1141.5049-1.01990.11151.0299-0.37890.47850.0410.15130.21350.00770.03660.279-0.0219-0.2925-0.13370.04780.03470.06060.26390.03750.333-9.2614-7.409778.5245
1153.23981.29370.81314.6382.46752.42280.22910.02620.32160.8617-0.20980.34050.5450.3201-0.00610.17540.00460.08250.1695-0.00980.156518.5992-22.602478.2684
1161.60390.4718-1.1412-0.1243-0.41920.8211-0.163-0.1307-0.1303-0.09090.0534-0.05680.09160.21370.08850.09130.03830.06370.12350.01740.22840.6836-31.560286.3136
1172.4515-0.749-0.84011.17920.6630.63250.25840.0462-0.02260.8431-0.18550.28511.2214-0.1808-0.6301-0.5670.17990.17930.0042-0.01670.1663-6.1644-19.28386.3003
1181.04640.0553-0.70490.7145-0.36681.23120.06230.00520.21270.02990.1035-0.0125-0.14650.171-0.29180.06260.04590.05630.14280.00530.18172.9333-11.607779.952
1190.8792-1.34320.07543.6957-0.02060.607-0.545-0.13110.4972-0.26760.4842-1.3486-0.14720.234-0.00130.12030.0358-0.02590.4520.04280.851139.878-22.200176.527
1200.7256-0.5042-0.29950.94190.30951.8948-0.0536-0.31740.05870.44460.0903-0.42640.03140.8545-0.04780.04190.02810.01240.415-0.02670.288914.0905-23.767888.9904
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:45)
2X-RAY DIFFRACTION2(chain A and resid 46:148)
3X-RAY DIFFRACTION3(chain A and resid 149:249)
4X-RAY DIFFRACTION4(chain A and resid 250:276)
5X-RAY DIFFRACTION5(chain B and resid 4:22)
6X-RAY DIFFRACTION6(chain B and resid 23:98)
7X-RAY DIFFRACTION7(chain B and resid 99:139)
8X-RAY DIFFRACTION8(chain B and resid 140:244)
9X-RAY DIFFRACTION9(chain C and resid 475:481)
10X-RAY DIFFRACTION10(chain C and resid 482:505)
11X-RAY DIFFRACTION11(chain D and resid 8:45)
12X-RAY DIFFRACTION12(chain D and resid 46:148)
13X-RAY DIFFRACTION13(chain D and resid 149:249)
14X-RAY DIFFRACTION14(chain D and resid 250:276)
15X-RAY DIFFRACTION15(chain E and resid 4:22)
16X-RAY DIFFRACTION16(chain E and resid 23:98)
17X-RAY DIFFRACTION17(chain E and resid 99:139)
18X-RAY DIFFRACTION18(chain E and resid 140:244)
19X-RAY DIFFRACTION19(chain F and resid 475:481)
20X-RAY DIFFRACTION20(chain F and resid 482:505)
21X-RAY DIFFRACTION21(chain G and resid 8:45)
22X-RAY DIFFRACTION22(chain G and resid 46:148)
23X-RAY DIFFRACTION23(chain G and resid 149:249)
24X-RAY DIFFRACTION24(chain G and resid 250:276)
25X-RAY DIFFRACTION25(chain H and resid 4:22)
26X-RAY DIFFRACTION26(chain H and resid 23:98)
27X-RAY DIFFRACTION27(chain H and resid 99:139)
28X-RAY DIFFRACTION28(chain H and resid 140:244)
29X-RAY DIFFRACTION29(chain I and resid 475:481)
30X-RAY DIFFRACTION30(chain I and resid 482:505)
31X-RAY DIFFRACTION31(chain J and resid 8:45)
32X-RAY DIFFRACTION32(chain J and resid 46:148)
33X-RAY DIFFRACTION33(chain J and resid 149:249)
34X-RAY DIFFRACTION34(chain J and resid 250:276)
35X-RAY DIFFRACTION35(chain K and resid 4:22)
36X-RAY DIFFRACTION36(chain K and resid 23:98)
37X-RAY DIFFRACTION37(chain K and resid 99:139)
38X-RAY DIFFRACTION38(chain K and resid 140:244)
39X-RAY DIFFRACTION39(chain L and resid 475:481)
40X-RAY DIFFRACTION40(chain L and resid 482:505)
41X-RAY DIFFRACTION41(chain M and resid 8:45)
42X-RAY DIFFRACTION42(chain M and resid 46:148)
43X-RAY DIFFRACTION43(chain M and resid 149:249)
44X-RAY DIFFRACTION44(chain M and resid 250:276)
45X-RAY DIFFRACTION45(chain N and resid 4:22)
46X-RAY DIFFRACTION46(chain N and resid 23:98)
47X-RAY DIFFRACTION47(chain N and resid 99:139)
48X-RAY DIFFRACTION48(chain N and resid 140:244)
49X-RAY DIFFRACTION49(chain O and resid 475:481)
50X-RAY DIFFRACTION50(chain O and resid 482:505)
51X-RAY DIFFRACTION51(chain P and resid 8:45)
52X-RAY DIFFRACTION52(chain P and resid 46:148)
53X-RAY DIFFRACTION53(chain P and resid 149:249)
54X-RAY DIFFRACTION54(chain P and resid 250:276)
55X-RAY DIFFRACTION55(chain Q and resid 4:22)
56X-RAY DIFFRACTION56(chain Q and resid 23:98)
57X-RAY DIFFRACTION57(chain Q and resid 99:139)
58X-RAY DIFFRACTION58(chain Q and resid 140:244)
59X-RAY DIFFRACTION59(chain R and resid 475:481)
60X-RAY DIFFRACTION60(chain R and resid 482:505)
61X-RAY DIFFRACTION61(chain S and resid 8:45)
62X-RAY DIFFRACTION62(chain S and resid 46:148)
63X-RAY DIFFRACTION63(chain S and resid 149:249)
64X-RAY DIFFRACTION64(chain S and resid 250:276)
65X-RAY DIFFRACTION65(chain T and resid 4:22)
66X-RAY DIFFRACTION66(chain T and resid 23:98)
67X-RAY DIFFRACTION67(chain T and resid 99:139)
68X-RAY DIFFRACTION68(chain T and resid 140:244)
69X-RAY DIFFRACTION69(chain U and resid 475:481)
70X-RAY DIFFRACTION70(chain U and resid 482:505)
71X-RAY DIFFRACTION71(chain V and resid 8:45)
72X-RAY DIFFRACTION72(chain V and resid 46:148)
73X-RAY DIFFRACTION73(chain V and resid 149:249)
74X-RAY DIFFRACTION74(chain V and resid 250:276)
75X-RAY DIFFRACTION75(chain W and resid 4:22)
76X-RAY DIFFRACTION76(chain W and resid 23:98)
77X-RAY DIFFRACTION77(chain W and resid 99:139)
78X-RAY DIFFRACTION78(chain W and resid 140:244)
79X-RAY DIFFRACTION79(chain X and resid 475:481)
80X-RAY DIFFRACTION80(chain X and resid 482:505)
81X-RAY DIFFRACTION81(chain Y and resid 8:45)
82X-RAY DIFFRACTION82(chain Y and resid 46:148)
83X-RAY DIFFRACTION83(chain Y and resid 149:249)
84X-RAY DIFFRACTION84(chain Y and resid 250:276)
85X-RAY DIFFRACTION85(chain Z and resid 4:22)
86X-RAY DIFFRACTION86(chain Z and resid 23:98)
87X-RAY DIFFRACTION87(chain Z and resid 99:139)
88X-RAY DIFFRACTION88(chain Z and resid 140:244)
89X-RAY DIFFRACTION89(chain 0 and resid 475:481)
90X-RAY DIFFRACTION90(chain 0 and resid 482:505)
91X-RAY DIFFRACTION91(chain 1 and resid 8:45)
92X-RAY DIFFRACTION92(chain 1 and resid 46:148)
93X-RAY DIFFRACTION93(chain 1 and resid 149:249)
94X-RAY DIFFRACTION94(chain 1 and resid 250:276)
95X-RAY DIFFRACTION95(chain 2 and resid 4:22)
96X-RAY DIFFRACTION96(chain 2 and resid 23:98)
97X-RAY DIFFRACTION97(chain 2 and resid 99:139)
98X-RAY DIFFRACTION98(chain 2 and resid 140:244)
99X-RAY DIFFRACTION99(chain 3 and resid 475:481)
100X-RAY DIFFRACTION100(chain 3 and resid 482:505)
101X-RAY DIFFRACTION101(chain 4 and resid 8:45)
102X-RAY DIFFRACTION102(chain 4 and resid 46:148)
103X-RAY DIFFRACTION103(chain 4 and resid 149:249)
104X-RAY DIFFRACTION104(chain 4 and resid 250:276)
105X-RAY DIFFRACTION105(chain 5 and resid 4:22)
106X-RAY DIFFRACTION106(chain 5 and resid 23:98)
107X-RAY DIFFRACTION107(chain 5 and resid 99:139)
108X-RAY DIFFRACTION108(chain 5 and resid 140:244)
109X-RAY DIFFRACTION109(chain 6 and resid 475:481)
110X-RAY DIFFRACTION110(chain 6 and resid 482:505)
111X-RAY DIFFRACTION111(chain 7 and resid 8:45)
112X-RAY DIFFRACTION112(chain 7 and resid 46:148)
113X-RAY DIFFRACTION113(chain 7 and resid 149:249)
114X-RAY DIFFRACTION114(chain 7 and resid 250:276)
115X-RAY DIFFRACTION115(chain 8 and resid 4:22)
116X-RAY DIFFRACTION116(chain 8 and resid 23:98)
117X-RAY DIFFRACTION117(chain 8 and resid 99:139)
118X-RAY DIFFRACTION118(chain 8 and resid 140:244)
119X-RAY DIFFRACTION119(chain 9 and resid 475:481)
120X-RAY DIFFRACTION120(chain 9 and resid 482:505)

+
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://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

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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。

-
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