[日本語] English
万見
- PDB-4aj5: Crystal structure of the Ska core complex -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4aj5
タイトルCrystal structure of the Ska core complex
要素
  • SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
  • SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
  • SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
キーワードCELL CYCLE / SKA COMPLEX / MITOSIS / CELL DIVISION / KINETOCHORE-MICROTUBULE ATTACHMENT / KMN NETWORK / NDC80 COMPLEX / DAM1/DASH
機能・相同性
機能・相同性情報


outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / intercellular bridge / centriolar satellite / regulation of microtubule polymerization or depolymerization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation ...outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / intercellular bridge / centriolar satellite / regulation of microtubule polymerization or depolymerization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / spindle microtubule / mitotic spindle / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / cell division / centrosome / cytosol
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1380 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1400 / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 3 / Ska2, N-terminal / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 1 / SKA1 microtubule binding domain / Spindle and kinetochore-associated protein 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1380 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1400 / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 3 / Ska2, N-terminal / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 1 / SKA1 microtubule binding domain / Spindle and kinetochore-associated protein 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
類似検索 - ドメイン・相同性
Spindle and kinetochore-associated protein 3 / Spindle and kinetochore-associated protein 2 / Spindle and kinetochore-associated protein 1
類似検索 - 構成要素
生物種HOMO SAPIENS (ヒト)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 3.32 Å
データ登録者Jeyaprakash, A.A. / Santamaria, A. / Jayachandran, U. / Chan, Y.W. / Benda, C. / Nigg, E.A. / Conti, E.
引用ジャーナル: Mol.Cell / 年: 2012
タイトル: Structural and Functional Organization of the Ska Complex, a Key Component of the Kinetochore-Microtubule Interface.
著者: Jeyaprakash, A.A. / Santamaria, A. / Jayachandran, U. / Chan, Y.W. / Benda, C. / Nigg, E.A. / Conti, E.
履歴
登録2012年2月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02012年5月23日Provider: repository / タイプ: Initial release

-
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

-
集合体

登録構造単位
1: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
2: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
3: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
4: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
A: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
B: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
C: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
D: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
E: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
F: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
G: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
H: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
I: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
J: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1
K: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
L: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
M: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
N: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
O: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
P: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
Q: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
R: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
S: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
T: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2
U: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
V: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
W: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
X: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
Y: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3
Z: SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3


分子量 (理論値)分子数
合計 (水以外)367,17030
ポリマ－367,17030
非ポリマー00
水00
1


  • 登録構造と同一
  • ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)174.400, 193.121, 198.267
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number5
Space group name H-MC121
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
12
22
32
42
52
62
72
82
92
102
13
23
33
43
53
63
73
83
93
103

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN K AND (RESSEQ 1:28 OR RESSEQ 43:50)
211CHAIN L AND (RESSEQ 0:28 OR RESSEQ 43:50)
311CHAIN M AND (RESSEQ 0:28 OR RESSEQ 43:50)
411CHAIN N AND (RESSEQ 1:28 OR RESSEQ 43:50)
511CHAIN O AND (RESSEQ 0:28 OR RESSEQ 43:50)
611CHAIN P AND (RESSEQ 0:28 OR RESSEQ 43:50)
711CHAIN Q AND (RESSEQ 0:28 OR RESSEQ 44:50)
811CHAIN R AND (RESSEQ 0:28 OR RESSEQ 43:50)
911CHAIN S AND (RESSEQ 0:28 OR RESSEQ 43:50)
1011CHAIN T AND (RESSEQ 0:28 OR RESSEQ 43:50)
112CHAIN E AND (RESSEQ 4:60)
212CHAIN H AND (RESSEQ 4:60)
312CHAIN A AND (RESSEQ 4:60)
412CHAIN B AND (RESSEQ 4:60)
512CHAIN C AND (RESSEQ 4:60)
612CHAIN D AND (RESSEQ 4:60)
712CHAIN F AND (RESSEQ 4:60)
812CHAIN G AND (RESSEQ 4:60)
912CHAIN I AND (RESSEQ 4:60)
1012CHAIN J AND (RESSEQ 4:60)
113CHAIN U AND (RESSEQ 5:50)
213CHAIN V AND (RESSEQ 5:50)
313CHAIN W AND (RESSEQ 5:50)
413CHAIN X AND (RESSEQ 5:50)
513CHAIN Y AND (RESSEQ 5:50)
613CHAIN Z AND (RESSEQ 5:50)
713CHAIN 1 AND (RESSEQ 5:50)
813CHAIN 2 AND (RESSEQ 5:50)
913CHAIN 3 AND (RESSEQ 5:50)
1013CHAIN 4 AND (RESSEQ 5:50)

NCSアンサンブル:
ID
1
2
3

NCS oper:
IDCodeMatrixベクター
1given(-0.1914, 0.7366, 0.6486), (0.7442, -0.322, 0.5853), (0.64, 0.5947, -0.4865)-56.36, 32.14, 33.92
2given(-0.2229, -0.7075, 0.6706), (-0.7543, -0.3106, -0.5785), (0.6176, -0.6348, -0.4644)16.24, 101.7, 95.52
3given(-0.9048, -0.3976, 0.1523), (-0.424, 0.8154, -0.3936), (0.03233, -0.4208, -0.906)31.12, 32.31, 111.7
4given(0.1927, 0.02632, 0.9809), (-0.02054, -0.9993, 0.03085), (0.981, -0.0261, -0.1921)-39.46, 100.9, 48.26
5given(-0.8856, 0.4441, 0.136), (0.4601, 0.7991, 0.3869), (0.06315, 0.4052, -0.91)-9.809, -11.54, 68.96
6given(-0.08628, 0.4421, -0.8928), (-0.4823, -0.8027, -0.3509), (-0.8717, 0.4003, 0.282)31.01, 113.4, 22.56
7given(0.5748, 0.728, -0.372), (-0.7692, 0.3262, -0.5495), (-0.2791, 0.602, 0.7481)-15.39, 67.63, -15.27
8given(0.5685, -0.7583, -0.319), (0.7448, 0.3097, 0.5911), (-0.3494, -0.5736, 0.7409)57.83, 0.2538, 44.5
9given(-0.08726, -0.4771, -0.8745), (0.4658, -0.7955, 0.3875), (-0.8806, -0.3735, 0.2916)76.13, 68.01, 60.75
10given(0.1219, 0.05025, 0.9913), (-0.04582, -0.9974, 0.05619), (0.9915, -0.05227, -0.1192)-44.03, 98.22, 46.97
11given(0.5982, 0.7193, -0.3531), (-0.7446, 0.3363, -0.5766), (-0.296, 0.6078, 0.7368)-16.49, 68.58, -15.52
12given(0.5718, -0.7347, -0.365), (0.7673, 0.3216, 0.5548), (-0.2902, -0.5973, 0.7477)57.03, -0.2158, 45.98
13given(-0.1177, -0.4862, -0.8659), (0.4411, -0.8068, 0.3931), (-0.8897, -0.3357, 0.3094)75.98, 68.38, 58.52
14given(-0.1182, 0.464, -0.8779), (-0.4785, -0.8013, -0.3591), (-0.8701, 0.3776, 0.3167)28.62, 112.3, 22.32
15given(-0.8732, 0.4711, 0.1246), (0.4829, 0.8026, 0.3501), (0.06491, 0.3659, -0.9284)-12.04, -11.76, 72.73
16given(-0.2372, 0.7033, 0.6702), (0.7253, -0.3308, 0.6038), (0.6463, 0.6293, -0.4316)-57.65, 31.14, 30.32
17given(-0.2321, -0.6965, 0.679), (-0.7392, -0.3275, -0.5886), (0.6323, -0.6385, -0.4388)13.99, 102.4, 94.15
18given(-0.8795, -0.4546, 0.141), (-0.4725, 0.7986, -0.3728), (0.05684, -0.3945, -0.9171)33.35, 32.4, 110.7
19given(0.19, -0.0807, 0.9785), (0.0534, -0.9943, -0.09238), (0.9803, 0.0698, -0.1847)-32.52, 104.9, 41.27
20given(0.5858, 0.7285, -0.3551), (-0.7587, 0.3388, -0.5564), (-0.285, 0.5953, 0.7512)-16.47, 68.1, -16.29
21given(0.6419, -0.7234, -0.2542), (0.6622, 0.3558, 0.6595), (-0.3866, -0.5917, 0.7074)54.71, -5.761, 46.2
22given(-0.1189, -0.5304, -0.8394), (0.4059, -0.7975, 0.4465), (-0.9062, -0.2876, 0.3101)78.65, 65.7, 55.27
23given(-0.1202, 0.4662, -0.8764), (-0.4819, -0.7993, -0.3591), (-0.8679, 0.3792, 0.3208)28.43, 112.6, 21.96
24given(-0.8505, 0.5119, 0.1208), (0.5225, 0.7961, 0.3054), (0.06016, 0.3229, -0.9445)-12.54, -9.386, 74.84
25given(-0.0919, 0.6972, 0.711), (0.813, -0.3598, 0.4579), (0.575, 0.6201, -0.5337)-55.76, 38.67, 33.91
26given(-0.2424, -0.7147, 0.6561), (-0.7111, -0.3292, -0.6213), (0.66, -0.6172, -0.4284)17.11, 104.2, 91.54
27given(-0.8999, -0.4248, 0.09881), (-0.4236, 0.7971, -0.4304), (0.1041, -0.4291, -0.8972)35.78, 35.32, 109.7

-
要素

#1: タンパク質
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 3 / SKA3


分子量: 11842.551 Da / 分子数: 10 / 断片: RESIDUES 1-101 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): GOLD / 参照: UniProt: Q8IX90
#2: タンパク質
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 1 / SKA1


分子量: 10468.828 Da / 分子数: 10 / 断片: RESIDUES 1-91 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): GOLD / 参照: UniProt: Q96BD8
#3: タンパク質
SPINDLE AND KINETOCHORE-ASSOCIATED PROTEIN 2 / SKA2 / PROTEIN FAM33A


分子量: 14405.579 Da / 分子数: 10 / 断片: RESIDUES 1-121 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): GOLD / 参照: UniProt: Q8WVK7
構成要素の詳細ENGINEERED RESIDUE IN CHAIN 1, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 2, VAL 58 TO ILE ...ENGINEERED RESIDUE IN CHAIN 1, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 2, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 3, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN 4, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN U, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN V, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN W, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN X, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN Y, VAL 58 TO ILE ENGINEERED RESIDUE IN CHAIN Z, VAL 58 TO ILE

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 4.93 Å3/Da / 溶媒含有率: 75 % / 解説: SE-MET DATA WERE USED TO CONFIRM SEQUENCE REGISTER
結晶化pH: 7.6 / 詳細: 50 MM TRIS PH 7.6, 0.2 M LITHIUM ACETATE, 45% MPD

-
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: X10SA / 波長: 0.978
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2010年6月17日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.978 Å / 相対比: 1
反射解像度: 3.3→86.8 Å / Num. obs: 91708 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / 冗長度: 1.7 % / Biso Wilson estimate: 104.39 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.4
反射 シェル解像度: 3.3→3.5 Å / 冗長度: 1.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.2 / % possible all: 94.1

-
解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
SCALAデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散
開始モデル: NONE

解像度: 3.32→69.031 Å / SU ML: 0.56 / σ(F): 1.33 / 位相誤差: 35.46 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2797 4572 5 %
Rwork0.2345 --
obs0.2368 90812 94.22 %
溶媒の処理減衰半径: 1.11 Å / VDWプローブ半径: 1.3 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 89 Å2 / ksol: 0.276 e/Å3
原子変位パラメータBiso mean: 140.2 Å2
Baniso -1Baniso -2Baniso -3
1-19.9554 Å20 Å2-53.9348 Å2
2---30.9808 Å20 Å2
3---11.0254 Å2
精密化ステップサイクル: LAST / 解像度: 3.32→69.031 Å
タンパク質核酸リガンド溶媒全体
原子数21691 0 0 0 21691
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00921893
X-RAY DIFFRACTIONf_angle_d1.28129666
X-RAY DIFFRACTIONf_dihedral_angle_d17.3857921
X-RAY DIFFRACTIONf_chiral_restr0.0843634
X-RAY DIFFRACTIONf_plane_restr0.0053859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11K296X-RAY DIFFRACTIONPOSITIONAL
12L296X-RAY DIFFRACTIONPOSITIONAL0.047
13M296X-RAY DIFFRACTIONPOSITIONAL0.045
14N296X-RAY DIFFRACTIONPOSITIONAL0.038
15O296X-RAY DIFFRACTIONPOSITIONAL0.046
16P296X-RAY DIFFRACTIONPOSITIONAL0.048
17Q289X-RAY DIFFRACTIONPOSITIONAL0.04
18R296X-RAY DIFFRACTIONPOSITIONAL0.049
19S288X-RAY DIFFRACTIONPOSITIONAL0.051
110T292X-RAY DIFFRACTIONPOSITIONAL0.04
21E435X-RAY DIFFRACTIONPOSITIONAL
22H435X-RAY DIFFRACTIONPOSITIONAL0.054
23A431X-RAY DIFFRACTIONPOSITIONAL0.039
24B439X-RAY DIFFRACTIONPOSITIONAL0.035
25C431X-RAY DIFFRACTIONPOSITIONAL0.036
26D435X-RAY DIFFRACTIONPOSITIONAL0.049
27F420X-RAY DIFFRACTIONPOSITIONAL0.047
28G439X-RAY DIFFRACTIONPOSITIONAL0.038
29I431X-RAY DIFFRACTIONPOSITIONAL0.045
210J431X-RAY DIFFRACTIONPOSITIONAL0.035
31U357X-RAY DIFFRACTIONPOSITIONAL
32V357X-RAY DIFFRACTIONPOSITIONAL0.041
33W357X-RAY DIFFRACTIONPOSITIONAL0.04
34X357X-RAY DIFFRACTIONPOSITIONAL0.042
35Y357X-RAY DIFFRACTIONPOSITIONAL0.042
36Z357X-RAY DIFFRACTIONPOSITIONAL0.041
371357X-RAY DIFFRACTIONPOSITIONAL0.04
382357X-RAY DIFFRACTIONPOSITIONAL0.061
393351X-RAY DIFFRACTIONPOSITIONAL0.041
3104357X-RAY DIFFRACTIONPOSITIONAL0.039
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.35770.55761530.52552862X-RAY DIFFRACTION94
3.3577-3.39720.47421470.43962843X-RAY DIFFRACTION94
3.3972-3.43870.43381510.39362848X-RAY DIFFRACTION93
3.4387-3.48220.44921570.35992783X-RAY DIFFRACTION93
3.4822-3.5280.42021530.33642850X-RAY DIFFRACTION93
3.528-3.57630.41541340.32562789X-RAY DIFFRACTION93
3.5763-3.62740.37821360.33152882X-RAY DIFFRACTION93
3.6274-3.68160.34041670.31232813X-RAY DIFFRACTION94
3.6816-3.73910.39231410.29542952X-RAY DIFFRACTION95
3.7391-3.80040.31821520.27722859X-RAY DIFFRACTION95
3.8004-3.86590.32631560.26292863X-RAY DIFFRACTION94
3.8659-3.93620.29561460.26162906X-RAY DIFFRACTION95
3.9362-4.01190.31111530.24972828X-RAY DIFFRACTION95
4.0119-4.09380.32411330.23262910X-RAY DIFFRACTION95
4.0938-4.18280.2451530.21652856X-RAY DIFFRACTION94
4.1828-4.28010.27651430.20372849X-RAY DIFFRACTION94
4.2801-4.38710.23781700.18762827X-RAY DIFFRACTION93
4.3871-4.50570.24711440.18232860X-RAY DIFFRACTION93
4.5057-4.63820.26621300.18062893X-RAY DIFFRACTION95
4.6382-4.78790.26621720.19372874X-RAY DIFFRACTION95
4.7879-4.9590.22791410.18262932X-RAY DIFFRACTION95
4.959-5.15750.22741740.18422822X-RAY DIFFRACTION94
5.1575-5.39210.35171470.25042936X-RAY DIFFRACTION95
5.3921-5.67630.37081660.3082862X-RAY DIFFRACTION94
5.6763-6.03170.37811540.31672843X-RAY DIFFRACTION94
6.0317-6.49710.33251870.29992928X-RAY DIFFRACTION96
6.4971-7.15030.29651510.27652932X-RAY DIFFRACTION96
7.1503-8.18360.26271600.20912934X-RAY DIFFRACTION95
8.1836-10.30490.15041430.14042934X-RAY DIFFRACTION95
10.3049-69.04590.20681580.19922970X-RAY DIFFRACTION95
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)
12.113-0.5848-0.07971.4091-0.37430.13020.09750.6805-0.4521-0.4701-0.2618-0.12880.17170.2681-0.05570.27960.07420.39631.0059-0.17090.816317.759220.134836.7943
20.03410.0240.02670.03790.00070.03620.34160.32510.324-0.22650.51630.3662-0.3601-0.4812-0.00092.01440.2748-0.36451.81980.00151.36394.927223.299412.323
30.0387-0.06810.16030.1928-0.37560.70960.26870.1912-0.25150.1128-0.21320.7142-0.6929-0.15120.00341.50410.1308-0.49241.01930.15441.2213-34.068548.3666-4.5256
42.4047-2.52943.02152.5512-3.05873.54381.351-0.246-1.0898-1.17910.05881.10521.4481-0.60711.25760.9474-0.1759-0.06730.89380.17220.9991-17.510934.613413.0117
51.6388-0.750.46820.6915-0.58310.48730.29980.5437-0.4803-0.4964-0.23470.0063-0.13220.214-0.00430.992-0.0176-0.15420.6844-0.02250.6534-7.073933.734813.0288
60.0445-0.02850.02320.04540.00650.02930.3928-0.6960.1694-0.0690.9524-0.17-0.16421.21060.00562.38430.3902-0.40621.4723-0.18251.3247-46.128165.6886-15.9767
70.3311-0.0072-0.241.6208-0.36450.9697-0.4557-0.98940.21570.58090.38540.1118-0.3019-0.6954-0.00191.2690.0007-0.03431.1337-0.18010.62871.065781.319156.9525
80.9205-0.7551-0.07041.4521-0.65340.79-0.12790.17520.3378-0.6432-0.40421.360.0988-0.06380.00311.8866-0.2425-0.7911.15290.43672.139-38.908155.298824.6378
90.5256-0.5984-0.56894.28241.54320.83860.10620.08220.1097-0.0794-0.0466-0.2876-0.02040.04630.10221.49330.1921-1.07951.76950.02972.4123-58.790742.6523-4.4935
100.1560.0736-0.05310.0487-0.01830.0739-0.34420.19680.70740.80190.0909-0.15070.718-0.23190.00111.7933-0.2057-0.62151.2712-0.21771.6326-61.664552.2084-2.178
110.85290.15331.25520.40610.67641.74740.81710.1218-0.7026-0.366-0.4744-0.03740.81990.19551.66490.6361-0.25340.02740.70430.14940.970317.42898.576637.2014
120.92930.13220.57710.2231-0.18890.8249-0.30770.36930.8331-0.3962-0.04550.0797-0.33310.1666-0.79910.38710.0818-0.04160.19890.05650.1211-0.934980.247520.7938
130.69170.5816-0.93980.5257-0.74641.32810.1209-0.2938-0.4232-0.2867-0.7324-0.01770.3513-0.1756-0.2012.163-0.2806-1.09061.6523-0.32232.1098-6.442122.729918.188
140.4153-0.34330.01260.31710.13620.7899-0.06320.41290.0969-0.393-0.0867-0.3177-0.25470.3409-0.74860.9079-0.19950.36320.96130.12250.23086.048375.420625.1647
151.3780.0441.01731.92540.94972.3356-0.3431-0.09970.4881-0.0734-0.21210.5744-0.15410.2987-0.21830.5437-0.32970.25420.850.39870.689659.377690.474266.9274
160.0006-0.0240.02450.3522-0.21590.5349-0.0020.1620.1674-0.213-0.0797-0.2390.03510.2762-0.68810.8011-0.48470.32150.87880.53560.635434.045873.176147.1
170.8713-0.2624-0.22191.07161.06461.83610.26470.1962-0.70470.575-0.30960.06180.19840.38860.00060.6571-0.2021-0.41231.0541-0.00151.338556.363116.673266.377
180.0280.0325-0.04690.45370.1460.1763-0.404-0.1348-0.37260.2384-0.20290.36150.6883-0.2303-0.01771.3130.1132-0.48511.39860.24962.484278.6755-5.937979.8488
190.03970.04060.09220.2480.00230.2566-0.08910.014-0.25520.1997-0.17170.0504-0.38380.0436-0.13122.5461-0.2116-1.24240.9832-0.01642.649172.30337.288878.1107
200.47960.67320.64521.1881-0.33041.98570.4358-0.0762-0.35550.6084-0.0919-0.20170.47260.51020.2610.0698-0.29730.10130.01480.24580.199815.196319.63769.1948
210.484-0.2224-0.33130.75871.08561.5540.1375-0.08120.06680.00050.6101-0.0187-0.1348-0.00180.22681.35710.0609-0.63361.15010.33451.420464.0393-4.4901106.1195
220.2368-0.048-0.09540.04020.09940.2488-0.13270.2362-0.4772-0.0144-0.50440.33560.0441-0.1015-0.01691.3696-0.1613-0.63112.4105-0.34671.542150.5606-2.986395.4997
231.9185-1.1630.53750.7593-0.04291.7190.1773-0.6940.43380.6309-0.46140.903-0.2698-0.4083-0.00090.59780.06710.23810.957-0.16741.0641-22.127958.837840.3068
241.61580.51031.25081.20630.06221.7561-0.20110.0119-0.5986-0.97440.52620.0829-0.2270.5418-0.01020.522-0.2580.17560.7740.19150.8822-15.4692-9.90641.9802
251.84990.37180.33311.1739-0.21780.470.0272-0.97850.10170.53820.31590.17410.10330.0120.03631.3499-0.2292-0.1231.01590.29050.656424.368159.658475.3538
260.0011-0.0063-0.00670.03550.03750.0392-0.336-0.43170.3816-0.25790.64060.2096-0.0919-0.14390.00911.80190.1629-0.50051.36870.30061.64527.228482.6274.6067
270.19510.1769-0.02470.4119-0.26790.2044-0.2386-0.0822-0.03-0.2486-0.0152-0.125-0.5143-0.0203-0.00171.7366-0.0943-0.1811.0196-0.09061.4192-9.9969108.40743.6094
280.1317-0.0484-0.06190.0301-0.00440.08770.25841.05370.0101-0.29810.2174-0.3253-0.332-0.21650.09721.40820.2592-0.90721.2016-0.23531.7668-22.0307138.751732.5584
290.05160.04750.02330.04550.03380.0890.0434-0.3958-0.18280.6197-0.43630.50340.05231.1169-0.00042.2522-0.0256-1.20891.2110.12172.3042-11.4031130.370541.2917
301.56270.4544-0.82330.9116-0.07431.69120.0503-0.39610.00330.2369-0.0960.05070.05830.1331-0.06850.5649-0.50020.28390.81810.3770.485315.80927.482471.0768
311.06640.17420.8942.34330.21581.47920.19720.1418-0.69560.75650.5332-1.3166-0.06050.20140.01830.98320.11030.0020.8256-0.20280.491245.38988.39190.175
321.91511.07430.7160.98630.43430.2882-0.24610.70530.19-0.95680.33650.8208-0.31250.18050.10770.94620.0308-0.55890.50850.18710.8046-26.982568.21727.7461
330.71880.73271.60150.86631.82673.48470.808-0.0734-0.73360.9555-0.31690.03611.3811-0.10110.18180.5865-0.1354-0.13840.75490.13881.052618.15036.678542.2912
343.69892.325-0.99943.0027-0.31586.4469-0.38970.39590.2061-0.0870.7160.5999-0.5053-0.7311-1.74370.52-0.15380.29670.98430.11140.4305-12.447746.880127.6294
350.3476-0.156-0.08180.7906-0.26710.16150.07680.21540.6240.45610.24871.3127-0.3115-0.2854-0.05281.29090.1509-0.49960.62460.191.4278-5.612898.066217.3221
360.0305-0.00190.00850.03060.02250.01980.06630.37510.1460.0094-0.2880.05640.05450.139-0.00551.95880.1111-0.36881.26310.02311.6812.3205149.830422.4074
372.9494-0.1583-0.23210.6026-1.31122.93380.5751-0.34840.78690.9316-0.65310.5834-0.73720.1644-0.34560.64940.07080.43220.76280.09210.50391.637577.707937.1117
380.27-0.110.29390.2578-0.03580.3634-0.3149-0.68351.2552-0.4754-0.07510.6547-0.296-0.6699-0.00280.9094-0.06480.02130.85710.06331.038237.057491.756951.0067
390.18730.389-0.15056.38890.00030.14180.3863-0.5279-0.20990.8148-0.3829-0.993-0.06140.4285-0.63590.7111-0.3680.37530.9932-0.00520.708780.22595.963176.4888
401.2009-1.4172-0.08782.85010.85010.4899-0.2185-0.7169-0.31451.29160.5359-0.50290.47810.288-0.15450.9489-0.2868-0.14440.95570.18080.724548.461444.23564.5947
410.00520.0431-0.02350.4192-0.20270.1071-0.72570.1259-0.67530.0937-0.41010.11880.1619-0.0431-0.00251.82170.2169-0.59291.41040.33692.130277.1274-18.291271.5246
420.85020.43041.39470.34910.58012.36340.66980.0104-0.3830.2678-0.2118-0.61651.00180.75472.11690.4066-0.3235-0.03440.37160.35350.785521.588412.712369.4125
430.60791.05430.04151.75040.0219-0.0964-0.24460.1418-0.0131-1.65040.33870.12390.309-0.0425-0.00111.2736-0.2117-0.18890.72640.1080.8355-19.017514.427336.6647
442.9385-0.49810.91350.0534-0.08620.4753-0.41490.12781.6243-0.2653-0.3058-0.8917-0.5752-0.0163-1.27860.8773-0.3526-0.03580.63460.21060.58647.146295.227555.1868
450.2539-0.5973-0.0471.52320.77841.3379-0.2086-0.14520.1520.15770.6001-0.8197-0.27860.05440.9120.3639-0.05320.20360.64260.12160.199738.503664.488382.8722
461.26420.88480.63912.2427-0.51981.1879-0.2428-0.06840.24530.39830.1517-0.1155-0.1384-0.37310.00060.4667-0.14480.13490.78920.1280.6719-20.454518.278644.8904
470.78730.95270.53421.26020.36440.77180.0187-0.5614-0.2866-0.40180.04061.0477-0.3254-0.59860.01481.2687-0.0641-0.45720.97230.08311.7754-28.880166.669636.7514
480.880.82540.77170.81180.59711.25210.10840.5952-0.6153-0.9133-0.03810.45080.15180.5266-0.00180.94320.1604-0.24460.875-0.2281.283718.958.291434.6339
490.77940.4028-0.21281.40180.55030.4371-0.20970.34290.18220.158-0.1196-1.3181-0.6377-0.2714-0.00891.3877-0.1677-0.31090.8810.32950.9030.333880.272217.714
500.81240.3614-0.12270.281-0.09790.11830.07910.11720.0571-0.0152-0.1635-0.0934-0.24680.22221.40620.4002-0.30370.25780.71650.45370.327536.558283.108944.8316
510.0877-0.32270.04471.1909-0.16520.0230.074-0.2034-0.29590.74210.54360.24620.3325-0.2239-0.0441.4062-0.3259-0.82241.37870.34681.465878.453684.246381.8734
520.4399-0.171-0.7541.4725-0.6281.88650.36610.1772-1.4486-0.7785-0.09420.0791-0.1990.29520.00421.2569-0.2999-0.20940.81990.16531.16235.0762.798651.476
532.1230.84841.11281.57451.68031.8150.1118-0.0371-1.02290.13030.3484-0.45750.47750.45230.71860.1637-0.10490.07020.94320.2851.210759.904129.278260.2018
540.0204-0.0061-0.02990.00190.0090.04390.4747-0.1618-0.11850.28310.10090.2831-0.0096-0.34110.00491.57010.4645-0.26551.7503-0.31792.631463.4836-9.215868.5972
551.6955-0.26940.6940.26510.2040.73890.0658-0.4275-0.69870.477-0.024-0.23560.02030.11680.01450.9535-0.3636-0.43480.64450.36530.804713.03117.08571.9265
560.0060.01040.01360.01760.0230.0303-0.31960.51740.1679-0.73930.0118-0.58870.31410.35120.00152.1799-0.3158-1.04252.59770.87363.228560.333914.9828104.5331
571.6799-1.41180.61311.9503-1.46681.391-0.5459-0.42110.66380.3024-0.06560.2765-1.4022-0.0576-0.0521.604-0.0616-0.58770.6736-0.11961.31780.104193.350358.0206
580.98250.51160.35952.44370.82140.8781-0.0683-0.69990.19950.6098-0.2421-0.1614-0.0934-0.2964-0.00120.70470.05180.00890.8023-0.00150.64330.93164.375684.6207
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN K AND (RESSEQ 1:32)
2X-RAY DIFFRACTION2CHAIN K AND (RESSEQ 33:43)
3X-RAY DIFFRACTION3CHAIN K AND (RESSEQ 44:113)
4X-RAY DIFFRACTION4CHAIN U
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 3:79)
6X-RAY DIFFRACTION6CHAIN E AND (RESSEQ 80:88)
7X-RAY DIFFRACTION7CHAIN L AND (RESSEQ 0:42)
8X-RAY DIFFRACTION8CHAIN L AND (RESSEQ 43:85)
9X-RAY DIFFRACTION9CHAIN L AND (RESSEQ 86:91)
10X-RAY DIFFRACTION10CHAIN L AND (RESSEQ 92:113)
11X-RAY DIFFRACTION11CHAIN M
12X-RAY DIFFRACTION12CHAIN N AND (RESSEQ 1:104)
13X-RAY DIFFRACTION13CHAIN N AND (RESSEQ 105:114)
14X-RAY DIFFRACTION14CHAIN O AND (RESSEQ 0:41)
15X-RAY DIFFRACTION15CHAIN O AND (RESSEQ 42:114)
16X-RAY DIFFRACTION16CHAIN P AND (RESSEQ 0:42)
17X-RAY DIFFRACTION17CHAIN P AND (RESSEQ 43:95)
18X-RAY DIFFRACTION18CHAIN P AND (RESSEQ 96:103)
19X-RAY DIFFRACTION19CHAIN P AND (RESSEQ 104:113)
20X-RAY DIFFRACTION20CHAIN Q AND (RESSEQ 0:95)
21X-RAY DIFFRACTION21CHAIN Q AND (RESSEQ 96:103)
22X-RAY DIFFRACTION22CHAIN Q AND (RESSEQ 104:112)
23X-RAY DIFFRACTION23CHAIN R AND (RESSEQ 0:42)
24X-RAY DIFFRACTION24CHAIN R AND (RESSEQ 43:113)
25X-RAY DIFFRACTION25CHAIN S AND (RESSEQ -1:32)
26X-RAY DIFFRACTION26CHAIN S AND (RESSEQ 33:45)
27X-RAY DIFFRACTION27CHAIN S AND (RESSEQ 46:94)
28X-RAY DIFFRACTION28CHAIN S AND (RESSEQ 95:103)
29X-RAY DIFFRACTION29CHAIN S AND (RESSEQ 104:113)
30X-RAY DIFFRACTION30CHAIN T AND (RESSEQ 0:42)
31X-RAY DIFFRACTION31CHAIN T AND (RESSEQ 43:116)
32X-RAY DIFFRACTION32CHAIN V
33X-RAY DIFFRACTION33CHAIN W
34X-RAY DIFFRACTION34CHAIN X AND (RESSEQ 3:34)
35X-RAY DIFFRACTION35CHAIN X AND (RESSEQ 35:95)
36X-RAY DIFFRACTION36CHAIN X AND (RESSEQ 96:100)
37X-RAY DIFFRACTION37CHAIN Y AND (RESSEQ 3:34)
38X-RAY DIFFRACTION38CHAIN Y AND (RESSEQ 35:73)
39X-RAY DIFFRACTION39CHAIN Y AND (RESSEQ 74:101)
40X-RAY DIFFRACTION40CHAIN Z AND (RESSEQ 3:91)
41X-RAY DIFFRACTION41CHAIN Z AND (RESSEQ 92:99)
42X-RAY DIFFRACTION42CHAIN 1
43X-RAY DIFFRACTION43CHAIN 2
44X-RAY DIFFRACTION44CHAIN 3
45X-RAY DIFFRACTION45CHAIN 4
46X-RAY DIFFRACTION46CHAIN H
47X-RAY DIFFRACTION47CHAIN A
48X-RAY DIFFRACTION48CHAIN B
49X-RAY DIFFRACTION49CHAIN C
50X-RAY DIFFRACTION50CHAIN D AND (RESSEQ 3:79)
51X-RAY DIFFRACTION51CHAIN D AND (RESSEQ 80:88)
52X-RAY DIFFRACTION52CHAIN F AND (RESSEQ 3:32)
53X-RAY DIFFRACTION53CHAIN F AND (RESSEQ 33:79)
54X-RAY DIFFRACTION54CHAIN F AND (RESSEQ 80:84)
55X-RAY DIFFRACTION55CHAIN G AND (RESSEQ 3:77)
56X-RAY DIFFRACTION56CHAIN G AND (RESSEQ 78:88)
57X-RAY DIFFRACTION57CHAIN I
58X-RAY DIFFRACTION58CHAIN J

+
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://pdbjlvh1.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

+
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。

-
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