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- PDB-4uv2: Structure of the curli transport lipoprotein CsgG in a non-lipida... -

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基本情報

登録情報
データベース: PDB / ID: 4uv2
タイトルStructure of the curli transport lipoprotein CsgG in a non-lipidated, pre-pore conformation
要素CURLI PRODUCTION TRANSPORT COMPONENT CSGG
キーワードTRANSPORT PROTEIN / OUTER MEMBRANE PROTEIN
機能・相同性
機能・相同性情報


curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / single-species biofilm formation / cell outer membrane / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane
類似検索 - 分子機能
Curli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / Prokaryotic membrane lipoprotein lipid attachment site profile.
類似検索 - ドメイン・相同性
Curli production assembly/transport component CsgG
類似検索 - 構成要素
生物種ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (大腸菌)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.8 Å
データ登録者Goyal, P. / Krasteva, P.V. / Gerven, N.V. / Gubellini, F. / Broeck, I.V.D. / Troupiotis-Tsailaki, A. / Jonckheere, W. / Pehau-Arnaudet, G. / Pinkner, J.S. / Chapman, M.R. ...Goyal, P. / Krasteva, P.V. / Gerven, N.V. / Gubellini, F. / Broeck, I.V.D. / Troupiotis-Tsailaki, A. / Jonckheere, W. / Pehau-Arnaudet, G. / Pinkner, J.S. / Chapman, M.R. / Hultgren, S.J. / Howorka, S. / Fronzes, R. / Remaut, H.
引用ジャーナル: Nature / 年: 2014
タイトル: Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG.
著者: Parveen Goyal / Petya V Krasteva / Nani Van Gerven / Francesca Gubellini / Imke Van den Broeck / Anastassia Troupiotis-Tsaïlaki / Wim Jonckheere / Gérard Péhau-Arnaudet / Jerome S Pinkner ...著者: Parveen Goyal / Petya V Krasteva / Nani Van Gerven / Francesca Gubellini / Imke Van den Broeck / Anastassia Troupiotis-Tsaïlaki / Wim Jonckheere / Gérard Péhau-Arnaudet / Jerome S Pinkner / Matthew R Chapman / Scott J Hultgren / Stefan Howorka / Rémi Fronzes / Han Remaut /
要旨: Curli are functional amyloid fibres that constitute the major protein component of the extracellular matrix in pellicle biofilms formed by Bacteroidetes and Proteobacteria (predominantly of the α ...Curli are functional amyloid fibres that constitute the major protein component of the extracellular matrix in pellicle biofilms formed by Bacteroidetes and Proteobacteria (predominantly of the α and γ classes). They provide a fitness advantage in pathogenic strains and induce a strong pro-inflammatory response during bacteraemia. Curli formation requires a dedicated protein secretion machinery comprising the outer membrane lipoprotein CsgG and two soluble accessory proteins, CsgE and CsgF. Here we report the X-ray structure of Escherichia coli CsgG in a non-lipidated, soluble form as well as in its native membrane-extracted conformation. CsgG forms an oligomeric transport complex composed of nine anticodon-binding-domain-like units that give rise to a 36-stranded β-barrel that traverses the bilayer and is connected to a cage-like vestibule in the periplasm. The transmembrane and periplasmic domains are separated by a 0.9-nm channel constriction composed of three stacked concentric phenylalanine, asparagine and tyrosine rings that may guide the extended polypeptide substrate through the secretion pore. The specificity factor CsgE forms a nonameric adaptor that binds and closes off the periplasmic face of the secretion channel, creating a 24,000 Å(3) pre-constriction chamber. Our structural, functional and electrophysiological analyses imply that CsgG is an ungated, non-selective protein secretion channel that is expected to employ a diffusion-based, entropy-driven transport mechanism.
履歴
登録2014年8月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年9月24日Provider: repository / タイプ: Initial release
改定 1.12014年12月17日Group: Database references

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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: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
B: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
C: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
D: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
E: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
F: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
G: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
H: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
I: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
J: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
K: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
L: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
M: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
N: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
O: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
P: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)466,80316
ポリマ－466,80316
非ポリマー00
水00
1
A: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
B: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
C: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
D: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
E: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
F: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
G: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
H: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)233,4028
ポリマ－233,4028
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area32460 Å2
ΔGint-247.6 kcal/mol
Surface area92790 Å2
手法PISA
2
I: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
J: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
K: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
L: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
M: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
N: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
O: CURLI PRODUCTION TRANSPORT COMPONENT CSGG
P: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)233,4028
ポリマ－233,4028
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area37900 Å2
ΔGint-143.9 kcal/mol
Surface area89190 Å2
手法PISA
3
A: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
B: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
C: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
D: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
E: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
F: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
9
G: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
10
H: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
11
I: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
12
J: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
13
K: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
14
L: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
15
M: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
16
N: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
17
O: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
18
P: CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量 (理論値)分子数
合計 (水以外)29,1751
ポリマ－29,1751
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)101.330, 103.600, 141.740
Angle α, β, γ (deg.)111.33, 90.55, 118.21
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(0.721, -0.653, -0.232), (0.692, 0.698, 0.184), (0.042, -0.294, 0.955)53.34159, -62.85626, 6.13827
2given(0.109, -0.86, -0.499), (0.988, 0.04, 0.147), (-0.106, -0.509, 0.854)127.02126, -70.55044, 30.65374
3given(-0.554, -0.525, -0.646), (0.729, -0.681, -0.071), (-0.403, -0.51, 0.76)182.90945, -19.27828, 60.27341
4given(-0.788, 0.132, -0.601), (0.106, -0.933, -0.343), (-0.606, -0.334, 0.722)185.703, 56.1778, 76.24419
5given(-0.521, 0.767, -0.375), (-0.57, -0.639, -0.516), (-0.635, -0.055, 0.77)134.32648, 117.07698, 69.20484
6given(0.113, 0.988, -0.108), (-0.872, 0.046, -0.487), (-0.476, 0.149, 0.867)59.09249, 125.42868, 45.12075
7given(0.763, 0.646, 0.038), (-0.617, 0.744, -0.255), (-0.193, 0.171, 0.966)4.18739, 73.1925, 14.9601
8given(0.419, -0.854, 0.309), (-0.846, -0.491, -0.207), (0.328, -0.175, -0.928)-7.7236, 86.08511, 262.58951

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要素

#1: タンパク質
CURLI PRODUCTION TRANSPORT COMPONENT CSGG


分子量: 29175.193 Da / 分子数: 16 / 由来タイプ: 組換発現 / 詳細: NON-LIPIDATED, SOLUBLE FORM
由来: (組換発現) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (大腸菌)
プラスミド: PASK-IBA2 / 発現宿主: ESCHERICHIA COLI B (大腸菌) / 株 (発現宿主): B834 / Variant (発現宿主): DE3 / 参照: UniProt: P0AEA2
配列の詳細MATURE CSGG, NON-LIPIDATED C1S MUTANT

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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: 2.48 Å3/Da / 溶媒含有率: 50 % / 解説: NONE
結晶化pH: 4.2
詳細: 100 MM SODIUM ACETATE PH 4.2, 8% PEG 4000, 100 MM SODIUM MALONATE PH 7.0

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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: Diamond / ビームライン: I04 / 波長: 0.9795
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2012年5月5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: 0.9795 Å / 相対比: 1
反射解像度: 2.8→30 Å / Num. obs: 112419 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / 冗長度: 11.2 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.82
反射 シェル解像度: 2.8→2.9 Å / 冗長度: 7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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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
XSCALEデータスケーリング
XSCALE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: 2.8→29.765 Å / SU ML: 0.35 / σ(F): 2.12 / 位相誤差: 23.79 / 立体化学のターゲット値: MLHL
詳細: DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY AND ARE INDICATED BY A 0 OCCUPANCY
Rfactor反射数%反射
Rfree0.2337 5620 5 %
Rwork0.1881 --
obs0.1903 112369 98.98 %
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
原子変位パラメータBiso mean: 57.3 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→29.765 Å
タンパク質核酸リガンド溶媒全体
原子数28853 0 0 0 28853
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0129326
X-RAY DIFFRACTIONf_angle_d1.31439767
X-RAY DIFFRACTIONf_dihedral_angle_d14.38210791
X-RAY DIFFRACTIONf_chiral_restr0.0574606
X-RAY DIFFRACTIONf_plane_restr0.0075141
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.32991750.27773542X-RAY DIFFRACTION98
2.8318-2.86510.31681800.25573476X-RAY DIFFRACTION98
2.8651-2.90.29022000.24043585X-RAY DIFFRACTION99
2.9-2.93670.31642050.24043493X-RAY DIFFRACTION98
2.9367-2.97530.28461860.22973586X-RAY DIFFRACTION99
2.9753-3.0160.2751980.22763524X-RAY DIFFRACTION99
3.016-3.05910.31481840.23433517X-RAY DIFFRACTION99
3.0591-3.10470.30181830.24163565X-RAY DIFFRACTION99
3.1047-3.15310.26221760.22363619X-RAY DIFFRACTION99
3.1531-3.20480.29951600.22313509X-RAY DIFFRACTION99
3.2048-3.260.26741950.22933592X-RAY DIFFRACTION99
3.26-3.31920.31191900.22373525X-RAY DIFFRACTION99
3.3192-3.38290.2861920.22753601X-RAY DIFFRACTION99
3.3829-3.45190.25672130.19593499X-RAY DIFFRACTION99
3.4519-3.52680.24631720.19863551X-RAY DIFFRACTION99
3.5268-3.60870.24231930.19133568X-RAY DIFFRACTION99
3.6087-3.69880.23361680.17823564X-RAY DIFFRACTION99
3.6988-3.79860.21051740.16143588X-RAY DIFFRACTION99
3.7986-3.91020.19011840.15723571X-RAY DIFFRACTION99
3.9102-4.03610.20991890.15843591X-RAY DIFFRACTION99
4.0361-4.180.19761990.1533531X-RAY DIFFRACTION99
4.18-4.34680.18541690.14633572X-RAY DIFFRACTION99
4.3468-4.5440.18331810.14133599X-RAY DIFFRACTION99
4.544-4.78270.19261970.14013556X-RAY DIFFRACTION99
4.7827-5.08090.20651870.1613617X-RAY DIFFRACTION99
5.0809-5.4710.22181960.18343545X-RAY DIFFRACTION100
5.471-6.01750.21171840.18243572X-RAY DIFFRACTION100
6.0175-6.87880.23161990.19063567X-RAY DIFFRACTION100
6.8788-8.63140.20121970.19163578X-RAY DIFFRACTION100
8.6314-29.76670.22141940.20193546X-RAY DIFFRACTION99
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)
11.2322-0.3955-2.03880.29070.9792.52460.17170.41350.2284-0.1074-0.07950.1463-0.2664-0.3961-0.05290.3280.043-0.03840.29340.09070.400444.407829.0934115.7749
23.288-0.59330.93541.44261.72717.4211-0.123-0.60930.53050.0874-0.181-0.1567-0.7548-0.3057-0.07650.36510.02840.00020.3011-0.00280.370343.821335.843140.4966
35.1022-0.2605-0.84112.98452.00283.3342-0.1761.77130.1848-0.9933-0.165-0.2704-0.80910.0031-0.0660.5957-0.0874-0.11510.91350.05910.386945.051327.281292.7678
43.59990.6542-2.01662.3551-0.24236.6951-0.1721.01090.5521-0.71920.18480.0982-0.5104-0.3072-0.10780.5358-0.0573-0.11820.53990.12590.50542.338628.731499.7031
55.901-0.4049-2.36083.04540.35635.91610.02430.85240.5086-0.4142-0.12460.634-0.4186-1.29480.03360.4770.0498-0.15880.65270.04740.581929.120229.8234106.3988
67.01941.0461-1.4332.8276-0.68659.5125-0.20530.77210.0213-0.11710.10.165-0.5279-0.95910.06430.29710.1074-0.0140.3298-0.01120.447131.5265.4896104.6473
79.46873.6555-6.32621.0076-1.66743.43540.24360.80790.7084-0.05140.10210.2609-0.1983-0.6555-0.28640.2969-0.0001-0.0590.38270.04430.394344.51569.3275105.136
83.84290.1778-0.57546.16694.4525.8589-0.0291-0.15090.27060.3509-0.16750.4205-0.1852-0.12920.13380.32050.0008-0.0120.23950.05540.251833.261318.1903131.2073
93.47470.3072-2.22233.9032-2.39115.74720.35740.6387-0.0344-0.64980.00420.0557-0.53840.2982-0.3260.48860.0085-0.10480.4876-0.11080.435346.54254.452388.6276
101.71371.4384-2.51964.4035-2.57843.3655-0.3460.4352-0.1464-0.87850.1429-0.11230.5489-0.52980.10870.3821-0.0406-0.08650.4105-0.07480.350642.70981.462298.4594
118.15952.9919-1.70382.05114.99425.08340.14591.08720.61310.0834-0.34970.5151-0.3664-0.17870.25480.6142-0.0215-0.14530.67650.06780.411339.940312.722686.021
123.28281.0116-3.26643.9684-1.26667.2894-0.2410.9591-0.2307-0.35350.08020.29860.3797-1.24110.00660.31690.0122-0.05370.6677-0.05820.466830.2211-2.3649100.1108
132.8040.4364-1.08572.55240.4914.6227-0.77440.6661-0.1677-0.67980.4358-0.09860.6018-0.41490.46170.6847-0.2727-0.01990.6472-0.12280.724243.5283-22.0215101.2855
142.53440.9612-2.35390.8449-0.81762.7853-0.12870.2287-0.2113-0.17670.0480.03140.2716-0.29720.06850.2547-0.0027-0.06060.25940.01860.291550.1439-5.4859111.9167
153.57520.0768-3.74292.49141.64665.04320.12180.276-0.487-0.2611-0.32250.8678-0.1688-0.6619-0.02590.4336-0.0346-0.02820.3569-0.00560.383630.8941-5.1948128.1642
163.62681.4682-1.04172.0983-1.53686.07920.3755-0.11530.10110.0437-0.05520.1316-0.49050.81670.07040.36160.05970.00330.2234-0.06240.362862.0367-10.3003102.2105
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1033.9162-0.3815-1.75732.71210.3785.79420.0718-0.0413-1.08860.0026-0.2856-0.40751.35161.09370.09091.0260.3479-0.01690.70130.0860.738283.5094-26.8683180.245
1044.5492-0.2512-2.38034.0036-2.27525.5979-0.177-0.2862-1.01730.5989-0.2415-0.00371.20870.42950.39180.93170.0239-0.10110.37060.04280.549259.7193-32.7431170.6285
1050.29860.0302-1.66432.25340.51435.037-0.2165-0.2618-0.16450.28040.0302-0.24321.19930.29510.1890.59010.0087-0.04140.30340.07590.374454.2901-21.5639176.3054
1062.06338.5585-8.55645.6704-4.83172.26170.35150.53130.23440.48360.1180.1624-0.7424-0.4926-0.49520.53110.1250.01910.40050.02530.293970.8218-8.7143159.0486
1072.42746.5225-6.35868.6878-5.04925.2049-0.61810.7917-0.30720.29320.52-0.5102-0.09890.5540.1130.47030.0673-0.01850.32080.00220.447577.8843-14.1795155.6887
1085.5071-2.0569-2.93954.63531.89985.98290.21030.0002-0.13280.695-0.17220.4983-1.4444-0.27240.03240.5112-0.1675-0.07380.27150.07930.57245.6979-25.9377178.0374
1092.82810.0516-0.77960.01050.00320.1974-0.6051-1.1656-0.3771-0.35330.46660.27671.6099-0.3940.01621.0313-0.0196-0.0330.85910.35060.798844.0283-39.041199.4866
1102.2441.3772-4.07733.2606-5.24132.2338-0.0062-0.5469-0.20770.4218-0.0651-0.16471.3372-0.28150.04610.9125-0.0462-0.01610.45510.13460.553149.9325-31.1481181.4442
1112.4339-3.607-4.15888.50899.05242.2182-0.51040.0138-0.3821-0.107-0.27510.63870.68080.03470.54040.9379-0.0630.03090.38580.11920.484253.3468-33.543174.3726
1124.46640.9471-2.09592.2788-2.06982.9893-0.63730.7131-1.8240.0851-0.18470.13141.9399-0.54230.83992.2377-0.12530.1620.39960.00840.905755.0295-45.0229166.3915
1130.92220.1164-0.77940.25050.63932.1779-0.1691-0.0077-0.3330.1072-0.02470.03890.7406-0.13030.23060.6178-0.0366-0.00080.29250.05940.408942.85-24.2578161.1919
1142.8507-0.1687-0.82282.8506-0.28956.44840.0163-0.4233-0.48250.3492-0.13370.14331.215-0.66390.01460.6668-0.21440.07110.48680.05220.544626.255-28.4084168.6874
1151.44980.9231.1431.71221.25691.75070.19680.1715-0.52780.42260.47370.00010.6513-1.8832-0.55410.5192-0.4564-0.03691.21040.19580.721614.0547-11.0947159.0892
1165.52270.6429-1.26264.78011.61595.43850.2096-0.5380.05770.427-0.19120.45470.2496-0.8539-0.03720.2868-0.10170.11530.343-0.00720.316528.2308-5.2792180.9812
1179.76764.85287.52698.17216.49787.12380.281-0.9513-0.66581.44230.99120.60311.8716-2.3418-1.03810.5306-0.35310.04750.82680.05140.470519.7571-12.3064161.7166
1184.38463.8716-0.62796.44121.5284.85390.2232-0.7553-1.18210.32890.0914-0.55820.78-1.5567-0.26530.5109-0.1764-0.13660.65350.14570.483120.5965-10.7929153.9876
1199.8641-6.7958-9.16152.15688.52919.7769-0.2462-0.4435-0.363-0.0545-0.02850.211-0.38330.6640.08710.3891-0.0789-0.040.28380.07380.306340.351-14.1296147.3233
1208.8994-5.2287-8.99066.24136.58799.30160.08250.7051-1.30250.1786-0.95830.52450.3765-0.41750.80840.3067-0.10640.0020.3692-0.00310.505336.1625-18.8495140.3663
1213.99790.2211-2.59434.79232.98035.4244-0.2203-1.12780.13620.4747-0.4017-0.0508-0.36081.6424-0.02070.27350.04810.06540.7308-0.05030.606119.0716-1.6715172.0089
1225.12783.1185-7.90786.2776-7.01292.1733-0.0626-0.1416-0.10480.9720.16830.3133-0.7228-1.3636-0.52390.5477-0.08970.04760.7663-0.04810.401815.6694-2.9882172.6654
1234.25883.516-6.16864.7909-4.21172.5509-0.19290.7639-0.02210.15320.72570.70980.2431-2.5725-0.90090.3946-0.03480.10660.8779-0.00710.650914.1197-0.8686165.5993
1245.50442.5734-5.20836.1716-2.39877.498-0.64220.5079-0.95220.2869-0.01450.3940.8996-1.19460.36061.029-0.27210.21390.94280.09140.736810.0179-16.7317180.7915
1255.48910.74711.1123.3028-0.04588.33190.1413-0.3188-0.1587-0.15960.38180.6640.0582-2.5421-0.64440.4585-0.12440.07041.08580.06360.56438.2394-6.6712159.3135
1263.43233.0272.23887.25510.41911.9706-0.6857-1.56890.19031.3843-0.05080.8592-0.8063-0.86390.79640.4479-0.19040.14952.14290.18010.92420.7577-5.6836163.2556
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 18 THROUGH 100 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 101 THROUGH 120 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 121 THROUGH 150 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 151 THROUGH 210 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 211 THROUGH 258 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 16 THROUGH 43 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 44 THROUGH 85 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 86 THROUGH 120 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 121 THROUGH 150 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 151 THROUGH 187 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 188 THROUGH 210 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 211 THROUGH 258 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 18 THROUGH 33 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 34 THROUGH 100 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 101 THROUGH 120 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 121 THROUGH 136 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 137 THROUGH 150 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 151 THROUGH 187 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 188 THROUGH 210 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 211 THROUGH 258 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 17 THROUGH 43 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 44 THROUGH 85 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 86 THROUGH 100 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 101 THROUGH 120 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 121 THROUGH 150 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 151 THROUGH 187 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 188 THROUGH 210 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 211 THROUGH 247 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 248 THROUGH 258 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 17 THROUGH 43 )
31X-RAY DIFFRACTION31CHAIN 'E' AND (RESID 44 THROUGH 85 )
32X-RAY DIFFRACTION32CHAIN 'E' AND (RESID 86 THROUGH 136 )
33X-RAY DIFFRACTION33CHAIN 'E' AND (RESID 137 THROUGH 198 )
34X-RAY DIFFRACTION34CHAIN 'E' AND (RESID 199 THROUGH 210 )
35X-RAY DIFFRACTION35CHAIN 'E' AND (RESID 211 THROUGH 257 )
36X-RAY DIFFRACTION36CHAIN 'F' AND (RESID 17 THROUGH 85 )
37X-RAY DIFFRACTION37CHAIN 'F' AND (RESID 86 THROUGH 150 )
38X-RAY DIFFRACTION38CHAIN 'F' AND (RESID 151 THROUGH 257 )
39X-RAY DIFFRACTION39CHAIN 'G' AND (RESID 17 THROUGH 43 )
40X-RAY DIFFRACTION40CHAIN 'G' AND (RESID 44 THROUGH 85 )
41X-RAY DIFFRACTION41CHAIN 'G' AND (RESID 86 THROUGH 100 )
42X-RAY DIFFRACTION42CHAIN 'G' AND (RESID 101 THROUGH 120 )
43X-RAY DIFFRACTION43CHAIN 'G' AND (RESID 121 THROUGH 150 )
44X-RAY DIFFRACTION44CHAIN 'G' AND (RESID 151 THROUGH 210 )
45X-RAY DIFFRACTION45CHAIN 'G' AND (RESID 211 THROUGH 257 )
46X-RAY DIFFRACTION46CHAIN 'H' AND (RESID 16 THROUGH 43 )
47X-RAY DIFFRACTION47CHAIN 'H' AND (RESID 44 THROUGH 85 )
48X-RAY DIFFRACTION48CHAIN 'H' AND (RESID 86 THROUGH 136 )
49X-RAY DIFFRACTION49CHAIN 'H' AND (RESID 137 THROUGH 150 )
50X-RAY DIFFRACTION50CHAIN 'H' AND (RESID 151 THROUGH 170 )
51X-RAY DIFFRACTION51CHAIN 'H' AND (RESID 171 THROUGH 187 )
52X-RAY DIFFRACTION52CHAIN 'H' AND (RESID 188 THROUGH 210 )
53X-RAY DIFFRACTION53CHAIN 'H' AND (RESID 211 THROUGH 258 )
54X-RAY DIFFRACTION54CHAIN 'I' AND (RESID 16 THROUGH 43 )
55X-RAY DIFFRACTION55CHAIN 'I' AND (RESID 44 THROUGH 63 )
56X-RAY DIFFRACTION56CHAIN 'I' AND (RESID 64 THROUGH 74 )
57X-RAY DIFFRACTION57CHAIN 'I' AND (RESID 75 THROUGH 85 )
58X-RAY DIFFRACTION58CHAIN 'I' AND (RESID 86 THROUGH 100 )
59X-RAY DIFFRACTION59CHAIN 'I' AND (RESID 101 THROUGH 120 )
60X-RAY DIFFRACTION60CHAIN 'I' AND (RESID 121 THROUGH 136 )
61X-RAY DIFFRACTION61CHAIN 'I' AND (RESID 137 THROUGH 150 )
62X-RAY DIFFRACTION62CHAIN 'I' AND (RESID 151 THROUGH 187 )
63X-RAY DIFFRACTION63CHAIN 'I' AND (RESID 188 THROUGH 210 )
64X-RAY DIFFRACTION64CHAIN 'I' AND (RESID 211 THROUGH 257 )
65X-RAY DIFFRACTION65CHAIN 'J' AND (RESID 17 THROUGH 43 )
66X-RAY DIFFRACTION66CHAIN 'J' AND (RESID 44 THROUGH 85 )
67X-RAY DIFFRACTION67CHAIN 'J' AND (RESID 86 THROUGH 100 )
68X-RAY DIFFRACTION68CHAIN 'J' AND (RESID 101 THROUGH 120 )
69X-RAY DIFFRACTION69CHAIN 'J' AND (RESID 121 THROUGH 151 )
70X-RAY DIFFRACTION70CHAIN 'J' AND (RESID 152 THROUGH 187 )
71X-RAY DIFFRACTION71CHAIN 'J' AND (RESID 188 THROUGH 210 )
72X-RAY DIFFRACTION72CHAIN 'J' AND (RESID 211 THROUGH 234 )
73X-RAY DIFFRACTION73CHAIN 'J' AND (RESID 235 THROUGH 257 )
74X-RAY DIFFRACTION74CHAIN 'K' AND (RESID 17 THROUGH 43 )
75X-RAY DIFFRACTION75CHAIN 'K' AND (RESID 44 THROUGH 85 )
76X-RAY DIFFRACTION76CHAIN 'K' AND (RESID 86 THROUGH 100 )
77X-RAY DIFFRACTION77CHAIN 'K' AND (RESID 101 THROUGH 120 )
78X-RAY DIFFRACTION78CHAIN 'K' AND (RESID 121 THROUGH 150 )
79X-RAY DIFFRACTION79CHAIN 'K' AND (RESID 151 THROUGH 210 )
80X-RAY DIFFRACTION80CHAIN 'K' AND (RESID 211 THROUGH 233 )
81X-RAY DIFFRACTION81CHAIN 'K' AND (RESID 234 THROUGH 257 )
82X-RAY DIFFRACTION82CHAIN 'L' AND (RESID 17 THROUGH 43 )
83X-RAY DIFFRACTION83CHAIN 'L' AND (RESID 44 THROUGH 63 )
84X-RAY DIFFRACTION84CHAIN 'L' AND (RESID 64 THROUGH 74 )
85X-RAY DIFFRACTION85CHAIN 'L' AND (RESID 75 THROUGH 85 )
86X-RAY DIFFRACTION86CHAIN 'L' AND (RESID 86 THROUGH 100 )
87X-RAY DIFFRACTION87CHAIN 'L' AND (RESID 101 THROUGH 120 )
88X-RAY DIFFRACTION88CHAIN 'L' AND (RESID 121 THROUGH 136 )
89X-RAY DIFFRACTION89CHAIN 'L' AND (RESID 137 THROUGH 150 )
90X-RAY DIFFRACTION90CHAIN 'L' AND (RESID 151 THROUGH 170 )
91X-RAY DIFFRACTION91CHAIN 'L' AND (RESID 171 THROUGH 210 )
92X-RAY DIFFRACTION92CHAIN 'L' AND (RESID 211 THROUGH 233 )
93X-RAY DIFFRACTION93CHAIN 'L' AND (RESID 234 THROUGH 257 )
94X-RAY DIFFRACTION94CHAIN 'M' AND (RESID 17 THROUGH 43 )
95X-RAY DIFFRACTION95CHAIN 'M' AND (RESID 44 THROUGH 63 )
96X-RAY DIFFRACTION96CHAIN 'M' AND (RESID 64 THROUGH 74 )
97X-RAY DIFFRACTION97CHAIN 'M' AND (RESID 75 THROUGH 100 )
98X-RAY DIFFRACTION98CHAIN 'M' AND (RESID 101 THROUGH 120 )
99X-RAY DIFFRACTION99CHAIN 'M' AND (RESID 121 THROUGH 133 )
100X-RAY DIFFRACTION100CHAIN 'M' AND (RESID 134 THROUGH 187 )
101X-RAY DIFFRACTION101CHAIN 'M' AND (RESID 188 THROUGH 210 )
102X-RAY DIFFRACTION102CHAIN 'M' AND (RESID 211 THROUGH 233 )
103X-RAY DIFFRACTION103CHAIN 'M' AND (RESID 234 THROUGH 257 )
104X-RAY DIFFRACTION104CHAIN 'N' AND (RESID 17 THROUGH 43 )
105X-RAY DIFFRACTION105CHAIN 'N' AND (RESID 44 THROUGH 85 )
106X-RAY DIFFRACTION106CHAIN 'N' AND (RESID 86 THROUGH 100 )
107X-RAY DIFFRACTION107CHAIN 'N' AND (RESID 101 THROUGH 120 )
108X-RAY DIFFRACTION108CHAIN 'N' AND (RESID 121 THROUGH 136 )
109X-RAY DIFFRACTION109CHAIN 'N' AND (RESID 137 THROUGH 150 )
110X-RAY DIFFRACTION110CHAIN 'N' AND (RESID 151 THROUGH 210 )
111X-RAY DIFFRACTION111CHAIN 'N' AND (RESID 211 THROUGH 233 )
112X-RAY DIFFRACTION112CHAIN 'N' AND (RESID 234 THROUGH 257 )
113X-RAY DIFFRACTION113CHAIN 'O' AND (RESID 17 THROUGH 120 )
114X-RAY DIFFRACTION114CHAIN 'O' AND (RESID 121 THROUGH 257 )
115X-RAY DIFFRACTION115CHAIN 'P' AND (RESID 17 THROUGH 43 )
116X-RAY DIFFRACTION116CHAIN 'P' AND (RESID 44 THROUGH 63 )
117X-RAY DIFFRACTION117CHAIN 'P' AND (RESID 64 THROUGH 74 )
118X-RAY DIFFRACTION118CHAIN 'P' AND (RESID 75 THROUGH 85 )
119X-RAY DIFFRACTION119CHAIN 'P' AND (RESID 86 THROUGH 100 )
120X-RAY DIFFRACTION120CHAIN 'P' AND (RESID 101 THROUGH 120 )
121X-RAY DIFFRACTION121CHAIN 'P' AND (RESID 121 THROUGH 135 )
122X-RAY DIFFRACTION122CHAIN 'P' AND (RESID 151 THROUGH 165 )
123X-RAY DIFFRACTION123CHAIN 'P' AND (RESID 166 THROUGH 184 )
124X-RAY DIFFRACTION124CHAIN 'P' AND (RESID 185 THROUGH 210 )
125X-RAY DIFFRACTION125CHAIN 'P' AND (RESID 211 THROUGH 247 )
126X-RAY DIFFRACTION126CHAIN 'P' AND (RESID 248 THROUGH 257 )

+
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

+
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