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- PDB-2x53: Structure of the phage p2 baseplate in its activated conformation... -

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基本情報

登録情報
データベース: PDB / ID: 2x53
タイトルStructure of the phage p2 baseplate in its activated conformation with Sr
要素
  • ORF15
  • ORF16
  • PUTATIVE RECEPTOR BINDING PROTEIN
キーワードVIRAL PROTEIN / BASEPLATE
機能・相同性
機能・相同性情報


symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell
類似検索 - 分子機能
Phage tail base-plate attachment protein, domain D1/D2 / Elongation Factor Tu (Ef-tu); domain 3 - #210 / Jelly Rolls - #880 / Phage tail base-plate attachment protein, domain D3 / Phage tail base-plate attachment protein, domain D4 / Phage tail proteins - horseshoe like beta roll fold / Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 ...Phage tail base-plate attachment protein, domain D1/D2 / Elongation Factor Tu (Ef-tu); domain 3 - #210 / Jelly Rolls - #880 / Phage tail base-plate attachment protein, domain D3 / Phage tail base-plate attachment protein, domain D4 / Phage tail proteins - horseshoe like beta roll fold / Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 / : / : / : / : / Distal tail protein, N-terminal domain / Phage tail base-plate attachment protein N-terminal barrel domain / Phage tail base-plate attachment protein C-terminal insertion domain / Phage tail base-plate attachment protein N0 domain / Phage tail base-plate attachment protein C-terminal barrel domain / Dit, C-terminal domain / Triple-stranded beta-helix / Phage fibre proteins / Phage tail base-plate Siphoviridae RBP, head domain / : / Lactococcus phage p2, Receptor binding protein, neck domain / : / Lactophage receptor-binding protein N-terminal shoulder domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / Adenovirus pIV-like, attachment domain / 3-Layer(bab) Sandwich / Elongation Factor Tu (Ef-tu); domain 3 / Roll / Jelly Rolls / Beta Barrel / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
STRONTIUM ION / Orf16 / Distal tail protein / Receptor binding protein / Receptor binding protein
類似検索 - 構成要素
生物種LACTOCOCCUS PHAGE P2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.9 Å
データ登録者Sciara, G. / Bebeacua, C. / Bron, P. / Tremblay, D. / Ortiz-Lombardia, M. / Lichiere, J. / van Heel, M. / Campanacci, V. / Moineau, S. / Cambillau, C.
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2010
タイトル: Structure of lactococcal phage p2 baseplate and its mechanism of activation.
著者: Giuliano Sciara / Cecilia Bebeacua / Patrick Bron / Denise Tremblay / Miguel Ortiz-Lombardia / Julie Lichière / Marin van Heel / Valérie Campanacci / Sylvain Moineau / Christian Cambillau /
要旨: Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their ...Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This approximately 1 MDa, Escherichia coli-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca(2+), a cation mandatory for infection, the RBPs rotated 200 degrees downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection.
履歴
登録2010年2月5日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02010年2月16日Provider: repository / タイプ: Initial release
改定 1.12011年5月7日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32017年12月20日Group: Database references / Structure summary / カテゴリ: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
改定 1.42019年11月13日Group: Data collection / Database references / Other / カテゴリ: pdbx_database_related / pdbx_database_status
Item: _pdbx_database_related.content_type / _pdbx_database_status.status_code_sf
改定 1.52023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
1: ORF16
A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: PUTATIVE RECEPTOR BINDING PROTEIN
E: PUTATIVE RECEPTOR BINDING PROTEIN
F: PUTATIVE RECEPTOR BINDING PROTEIN
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: PUTATIVE RECEPTOR BINDING PROTEIN
K: PUTATIVE RECEPTOR BINDING PROTEIN
L: PUTATIVE RECEPTOR BINDING PROTEIN
M: PUTATIVE RECEPTOR BINDING PROTEIN
N: PUTATIVE RECEPTOR BINDING PROTEIN
O: PUTATIVE RECEPTOR BINDING PROTEIN
P: PUTATIVE RECEPTOR BINDING PROTEIN
Q: PUTATIVE RECEPTOR BINDING PROTEIN
R: PUTATIVE RECEPTOR BINDING PROTEIN
S: ORF15
T: ORF15
U: ORF15
V: ORF15
W: ORF15
X: ORF15
Y: ORF16
Z: ORF16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)849,42433
ポリマ－848,89827
非ポリマー5266
水00
1
1: ORF16
A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: PUTATIVE RECEPTOR BINDING PROTEIN
E: PUTATIVE RECEPTOR BINDING PROTEIN
F: PUTATIVE RECEPTOR BINDING PROTEIN
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: PUTATIVE RECEPTOR BINDING PROTEIN
K: PUTATIVE RECEPTOR BINDING PROTEIN
L: PUTATIVE RECEPTOR BINDING PROTEIN
M: PUTATIVE RECEPTOR BINDING PROTEIN
N: PUTATIVE RECEPTOR BINDING PROTEIN
O: PUTATIVE RECEPTOR BINDING PROTEIN
P: PUTATIVE RECEPTOR BINDING PROTEIN
Q: PUTATIVE RECEPTOR BINDING PROTEIN
R: PUTATIVE RECEPTOR BINDING PROTEIN
S: ORF15
T: ORF15
U: ORF15
V: ORF15
W: ORF15
X: ORF15
Y: ORF16
Z: ORF16
ヘテロ分子

1: ORF16
A: PUTATIVE RECEPTOR BINDING PROTEIN
B: PUTATIVE RECEPTOR BINDING PROTEIN
C: PUTATIVE RECEPTOR BINDING PROTEIN
D: PUTATIVE RECEPTOR BINDING PROTEIN
E: PUTATIVE RECEPTOR BINDING PROTEIN
F: PUTATIVE RECEPTOR BINDING PROTEIN
G: PUTATIVE RECEPTOR BINDING PROTEIN
H: PUTATIVE RECEPTOR BINDING PROTEIN
I: PUTATIVE RECEPTOR BINDING PROTEIN
J: PUTATIVE RECEPTOR BINDING PROTEIN
K: PUTATIVE RECEPTOR BINDING PROTEIN
L: PUTATIVE RECEPTOR BINDING PROTEIN
M: PUTATIVE RECEPTOR BINDING PROTEIN
N: PUTATIVE RECEPTOR BINDING PROTEIN
O: PUTATIVE RECEPTOR BINDING PROTEIN
P: PUTATIVE RECEPTOR BINDING PROTEIN
Q: PUTATIVE RECEPTOR BINDING PROTEIN
R: PUTATIVE RECEPTOR BINDING PROTEIN
S: ORF15
T: ORF15
U: ORF15
V: ORF15
W: ORF15
X: ORF15
Y: ORF16
Z: ORF16
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,698,84866
ポリマ－1,697,79754
非ポリマー1,05112
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area329180 Å2
ΔGint-2011.2 kcal/mol
Surface area566660 Å2
手法PISA
単位格子
Length a, b, c (Å)300.278, 239.511, 274.782
Angle α, β, γ (deg.)90.00, 124.36, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質 ORF16


分子量: 42869.238 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) LACTOCOCCUS PHAGE P2 (ウイルス) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: D3KFX5*PLUS
#2: タンパク質
PUTATIVE RECEPTOR BINDING PROTEIN / ORF18


分子量: 28536.861 Da / 分子数: 18 / Fragment: RESIDUES 2-264 / 由来タイプ: 組換発現 / 由来: (組換発現) LACTOCOCCUS PHAGE P2 (ウイルス) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q1RNF7, UniProt: Q71AW2*PLUS
#3: タンパク質
ORF15


分子量: 34437.848 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) LACTOCOCCUS PHAGE P2 (ウイルス) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: D3WAD3*PLUS
#4: 化合物
ChemComp-SR / STRONTIUM ION / ストロンチウムジカチオン


分子量: 87.620 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Sr
非ポリマーの詳細STRONTIUM (SR): DIVALENT CATION
配列の詳細THE SEQUENCE OF THIS PHAGE IS AVAILABLE FROM GENBANK ENTRY: GQ979703

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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: 4.52 Å3/Da / 溶媒含有率: 73 % / 解説: NONE
結晶化pH: 7.5
詳細: 20C, PROTEIN 4 MG/ML. 3.3% PEG 8000 IN 33 MM TRIS PH 8.5, 130 MM SR ACETATE, 66 MM LI SULFATE, AND 66 MM IMIDAZOLE.

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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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.98
検出器タイプ: ADSC CCD / 検出器: CCD
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: 0.98 Å / 相対比: 1
反射解像度: 3.9→120 Å / Num. obs: 141311 / % possible obs: 97 % / Observed criterion σ(I): 0 / 冗長度: 3 % / Biso Wilson estimate: 60.35 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.4
反射 シェル解像度: 3.9→4.1 Å / 冗長度: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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解析

ソフトウェア
名称バージョン分類
BUSTER2.9.2精密化
XDSデータ削減
SCALAデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2WZP

2wzp


解像度: 3.9→39.31 Å / Cor.coef. Fo:Fc: 0.8612 / Cor.coef. Fo:Fc free: 0.8407 / 交差検証法: THROUGHOUT / σ(F): 0
詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=SR. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=59736. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=SR. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=59736. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
Rfactor反射数%反射Selection details
Rfree0.2417 4226 2.99 %RANDOM
Rwork0.2293 ---
obs0.2296 141150 --
原子変位パラメータBiso mean: 110.08 Å2
Baniso -1Baniso -2Baniso -3
1--2.0172 Å20 Å221.4481 Å2
2--1.8721 Å20 Å2
3---0.1451 Å2
Refine analyzeLuzzati coordinate error obs: 0.995 Å
精密化ステップサイクル: LAST / 解像度: 3.9→39.31 Å
タンパク質核酸リガンド溶媒全体
原子数59736 0 6 0 59742
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00760981HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0382911HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d20799SINUSOIDAL3
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1662HARMONIC2
X-RAY DIFFRACTIONt_gen_planes8739HARMONIC5
X-RAY DIFFRACTIONt_it60981HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion18.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion8376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact65376SEMIHARMONIC4
LS精密化 シェル解像度: 3.9→4 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.253 296 2.82 %
Rwork0.2607 10215 -
all0.2604 10511 -
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)
12.0954-0.5903-0.82041.21430.83871.4415-0.08110.05850.14770.0616-0.02270.10480.06330.03330.1037-0.0410.2345-0.0009-0.32320.18710.149517.377856.565790.2489
22.83110.05561.15371.0844-1.1391.0260.0424-0.0226-0.07120.087-0.11120.0398-0.01290.0430.06880.01820.4067-0.0346-0.0722-0.05630.1443-21.038558.69958.946
31.27122.0267-0.1872.0618-0.39050.02870.06610.00040.03190.0031-0.0171-0.1115-0.0249-0.1707-0.049-0.16080.20480.13050.0375-0.05940.3899-5.5366.5874102.1878
40.849-1.25040.42311.9474-0.29582.0446-0.02330.06950.01180.0769-0.0705-0.0254-0.07290.00340.0938-0.03820.2517-0.183-0.13940.17050.257-16.937976.168454.973
5-0.2261-1.37710.24594.3662-1.77460.4419-0.04120.1370.16350.03210.0128-0.032-0.0463-0.06060.0283-0.07440.20820.1048-0.21480.0540.496413.073783.643290.8286
61.3284-0.1424-0.14491.3709-0.06841.3273-0.01010.16570.09650.06830.0235-0.0598-0.03590.0428-0.0134-0.10290.33250.08240.12480.04680.071-5.683562.615749.4849
72.16592.064-0.72474.7874-2.27780.9809-0.0820.1573-0.05580.1807-0.09750.30650.0760.04270.1794-0.3311-0.0312-0.1217-0.06770.17660.4161-9.7061-2.5623104.1539
8-1.72110.36053.089503.75175.1287-0.02350.0669-0.0406-0.14510.0072-0.06820.0508-0.01910.01630.0825-0.133-0.23390.44860.14610.3527-40.3679-15.048766.8991
90.67090.85-0.29934.49341.5731-0.55990.13630.13980.13340.16250.09330.1237-0.1162-0.1655-0.2296-0.2579-0.125-0.1106-0.07380.16820.4806-29.7048-19.8179112.2253
10-0.85060.50643.40980-2.48585.0601-0.02040.0350.0067-0.08790.03310.10030.0366-0.0832-0.0128-0.18080.1494-0.35570.39560.23460.4034-51.5266-1.178671.5374
114.5615-3.2226-0.60080-0.3502-2.9537-0.02090.04150.0950.06130.05810.0627-0.0954-0.101-0.0371-0.25950.21420.032-0.19730.09740.368-33.29537.5508114.3677
12-0.1890.01921.81380-3.66483.94410.04220.0265-0.1208-0.1571-0.0293-0.0124-0.01630.0051-0.01290.17780.1075-0.25130.38030.33220.2414-34.83752.413664.5353
13-0.02890.1814-0.15263.5060.57310.7621-0.1790.1341-0.01190.0323-0.0077-0.02990.1869-0.15310.1867-0.0034-0.1381-0.0273-0.2052-0.33660.245821.4467-59.616587.2455
14-0.40420.94822.100601.88454.23560.03530.05690.0222-0.04850.0069-0.0770.00310.0719-0.04220.3528-0.1076-0.22990.2287-0.2880.12893.877-72.809342.8802
15-1.9955-0.01010.777202.32271.99550.00970.0313-0.0492-0.00780.08450.09790.07070.0238-0.09420.2912-0.17590.0203-0.3858-0.28130.179624.6657-86.708482.612
16-0.5270.80572.931100.66274.25420.0792-0.0454-0.0124-0.0644-0.02960.1425-0.0354-0.0294-0.04960.256-0.1324-0.2740.2844-0.29960.2927-12.3713-76.918550.4858
172.62884.1039-0.97320-0.1744-2.5209-0.0426-0.0628-0.0106-0.00450.03840.0364-0.0013-0.17760.0042-0.1722-0.37890.0369-0.40680.01560.43922.2674-77.371496.0493
18-1.4242-0.64772.42241.7927-2.55633.9780.08590.09570.0151-0.0083-0.02230.0077-0.124-0.0728-0.06360.3094-0.2022-0.23930.2471-0.11670.2898-6.7366-59.377549.7817
190.09130.07510.30633.57132.25360.88470.0951-0.1047-0.2159-0.0793-0.01340.05080.123-0.038-0.08180.42450.2042-0.1598-0.3093-0.2286-0.103479.5978-82.988846.4558
203.3712-1.48782.51041.04-0.40782.1824-0.00590.04790.0493-0.00580.00970.098-0.0124-0.0972-0.00380.13020.1172-0.37950.1924-0.2881-0.198150.172-59.625114.0119
212.6102-1.1435-0.88872.1494-0.24471.9018-0.02420.05640.1044-0.0125-0.0419-0.09090.0351-0.00520.06610.21480.1339-0.2466-0.2341-0.2766-0.245577.6805-56.038651.9063
220.45950.1231.8380.58250.98853.22580.00350.03390.1083-0.16490.0326-0.1608-0.05340.0338-0.03610.15250.1798-0.15650.18320.1076-0.37864.8386-55.20343.8053
230.96120.34440.01870.6896-0.88460.2297-0.00460.362-0.0150.15780.05680.09310.08230.1399-0.05220.37350.1837-0.13540.0321-0.2426-0.173498.0944-65.520935.7187
241.2755-0.98511.60643.41021.74483.61440.01060.1571-0.11280.0696-0.1591-0.121-0.0045-0.01810.14840.169-0.0719-0.13080.2077-0.4173-0.381559.4455-72.80645.0267
252.9065-2.2135-2.26580.11171.31592.52340.1817-0.0334-0.12650.00550.0202-0.1630.05440.0574-0.20190.30910.36990.42790.213-0.0024-0.1162126.1372-6.430921.5821
261.2298-0.44780.02530.40310.56822.39790.0434-0.1333-0.0368-0.09180.02230.08770.00060.0444-0.06560.67250.08390.1596-0.23260.4158-0.104384.3444-2.6854-5.1939
271.57920.4935-0.70042.6629-0.94360.79450.09610-0.0091-0.0528-0.15270.06090.064-0.04960.05650.42010.25780.31610.060.1615-0.4536105.09492.899236.8103
28-1.2776-0.56981.75770.74420.71834.0149-0.0674-0.11630.1291-0.05040.0850.0162-0.01220.0992-0.01760.56720.08020.1362-0.15420.4213-0.191388.296214.949-8.675
29-0.4697-0.81550.45582.51-2.40030.8427-0.08640.0590.01610.01030.01640.0301-0.00710.12560.070.19010.13350.350.19940.243-0.1462121.948420.728223.7559
30-2.77150.24441.23510-0.27773.4324-0.05430.0386-0.0302-0.03870.0585-0.04410.02950.1012-0.00420.49290.16070.26030.11130.1491-0.362398.74021.5772-15.9266
310.5278-1.30240.17184.28330.62731.14530.01980.1250.18070.03890.01930.01630.01790.0509-0.03910.26590.07940.2351-0.1990.42250.120174.003558.777755.0793
321.5281-0.43712.18960-1.38372.2798-0.01810.0756-0.0401-0.018-0.02650.16620.0215-0.11790.04460.41750.2543-0.15180.24890.16660.184443.284673.211218.8347
330.2307-2.7562-0.20593.6605-1.88440.178-0.0288-0.05990.0698-0.13520.0349-0.0376-0.0789-0.054-0.00610.46730.07940.1924-0.36030.42250.237169.101886.126655.5533
34-0.91110.35221.41520.1685-1.46027.16320.00630.0432-0.1312-0.0622-0.05420.02130.00790.02140.04790.50580.1499-0.10810.28550.31930.001457.724376.83527.9856
350.31262.1253-0.85591.8385-5.59811.8350.04120.06360.0283-0.02620.03090.0279-0.05110.1638-0.07210.22640.07370.3337-0.17560.41860.089590.95176.006341.6379
36-2.12041.21711.83630.11332.17534.34590.02840.1101-0.060.02250.00330.07620.0014-0.1052-0.03170.43530.2385-0.04480.28520.11590.105253.789659.376812.5784
370.70080.4624-0.73792.6141-1.45353.87450.0970.0469-0.1241-0.0138-0.13770.0902-0.0519-0.13850.0407-0.19340.0329-0.0816-0.3347-0.021-0.077239.327411.4181110.6457
38-0.0985-1.82160.03840.7799-0.88180.0985-0.0776-0.22350.2434-0.01730.2492-0.0093-0.0306-0.0065-0.1716-0.29780.11550.0102-0.25270.04970.062816.148836.6514102.8233
392.0742-0.81150.82072.02020.0371.1727-0.0080.08630.00180.0270.01580.04250.1263-0.1589-0.0078-0.1718-0.08740.0199-0.2265-0.0156-0.128842.3554-18.0025108.8131
401.28410.1946-0.07640.0078-0.55560.078-0.01120.17260.01660.25730.09450.22750.06920.0263-0.0834-0.2446-0.0777-0.0313-0.0575-0.01010.33896.7965-19.3552107.4008
411.73190.11061.15480-0.34781.7047-0.0283-0.0375-0.0163-0.0493-0.059-0.03420.1072-0.05730.0873-0.01280.0093-0.0759-0.4065-0.0096-0.058465.7467-29.572494.8041
420.5907-0.7634-0.08710.37210.08271.52660.10630.1444-0.14710.1419-0.12420.06530.10170.09720.01790.1525-0.0311-0.2024-0.435-0.18490.044944.6036-56.085785.4327
432.07870.91810.1812.78670.15321.58060.20790.1912-0.0302-0.069-0.10550.1782-0.0986-0.0199-0.1024-0.1430.146-0.0294-0.2944-0.0005-0.259186.2295-11.816682.5702
440.1370.0288-0.16152.47080.5860.17920.0109-0.0489-0.0729-0.02220.02070.0074-0.08020.1373-0.03160.24180.2149-0.2275-0.0771-0.0559-0.233390.2278-36.878257.4182
451.2048-0.41670.85812.45320.52552.0111-0.02090.05330.24830.03220.1120.09080.00230.0118-0.0911-0.20260.11970.0433-0.17080.0775-0.197583.12217.514184.4311
46-0.02580.7826-0.503600.35041.5283-0.0018-0.10190.03640.1045-0.01210.02130.020.00340.014-0.07730.18550.1394-0.01210.2673-0.221899.026619.253152.7538
472.1344-0.0157-0.31210-0.5222.5391-0.02220.01150.006-0.081-0.05480.1893-0.04410.04250.0769-0.05610.0102-0.0459-0.44330.0645-0.002459.718929.133698.5321
48-0.15640.59540.01070.30270.130.85630.090.01870.0288-0.0293-0.1188-0.006-0.0864-0.160.02880.00360.2140.151-0.14910.22560.208761.908355.844975.1698
490.76271.3490.20552.6548-0.23960.49350.04840.0236-0.0583-0.3171-0.01760.09970.0347-0.0349-0.0308-0.09990.2464-0.1759-0.13080.1004-0.018820.433523.42968.8089
505.2141-3.35721.7035.355-3.08421.19410.03210.2048-0.0387-0.0446-0.01260.09270.0216-0.1032-0.01950.17580.2543-0.22380.06520.1395-0.10145.588519.3730.8576
511.4713-0.60860.7491.8455-1.14470.33650.08480.058-0.0298-0.042-0.08620.0844-0.0496-0.00230.0013-0.01740.26440.0153-0.01390.12160.038938.820832.448767.2034
520.09530.6884-0.58180.3440.6343.0445-0.00970.2410.1276-0.17940.16340.28180.0461-0.2-0.15380.06750.1046-0.359-0.0486-0.1581-0.076131.7135-31.285762.0086
531.18551.92210.99422.10631.84.77510.00160.0297-0.0605-0.1638-0.01410.04010.0346-0.0130.01250.08890.0469-0.22850.08690.0479-0.0657.09736.304453.9734
542.73881.5656-0.11401.9761-0.2682-0.00340.04880.0005-0.02370.03190.02160.0025-0.0459-0.0285-0.12040.1313-0.052-0.01-0.07170.104521.9278-21.411777.2396
550.6121-0.221-0.12922.5286-0.10841.22070.00360.3793-0.0859-0.0148-0.00060.19030.0219-0.0339-0.00290.08820.3134-0.13460.05010.0801-0.299766.55127.4841.0571
560.4402-2.97030.92452.1291-0.52475.8178-0.07270.090.0694-0.05750.0852-0.02020.0338-0.047-0.01260.09010.198-0.22170.2126-0.0771-0.271236.13-26.11136.525
57-2.9173-3.23351.01671.13170.58263.26710.02510.13350.01270.03030.00380.01520.0052-0.0738-0.02890.1170.2829-0.0928-0.0546-0.0153-0.194370.3007-11.421748.2724
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A 2 - A 141)
2X-RAY DIFFRACTION2(A 142 - A 264)
3X-RAY DIFFRACTION3(B 2 - B 141)
4X-RAY DIFFRACTION4(B 142 - B 264)
5X-RAY DIFFRACTION5(C 2 - C 141)
6X-RAY DIFFRACTION6(C 142 - C 264)
7X-RAY DIFFRACTION7(D 2 - D 141)
8X-RAY DIFFRACTION8(D 142 - D 264)
9X-RAY DIFFRACTION9(E 2 - E 141)
10X-RAY DIFFRACTION10(E 142 - E 264)
11X-RAY DIFFRACTION11(F 2 - F 141)
12X-RAY DIFFRACTION12(F 142 - F 264)
13X-RAY DIFFRACTION13(G 2 - G 141)
14X-RAY DIFFRACTION14(G 142 - G 264)
15X-RAY DIFFRACTION15(H 2 - H 141)
16X-RAY DIFFRACTION16(H 142 - H 264)
17X-RAY DIFFRACTION17(I 2 - I 141)
18X-RAY DIFFRACTION18(I 142 - I 264)
19X-RAY DIFFRACTION19(J 2 - J 141)
20X-RAY DIFFRACTION20(J 142 - J 264)
21X-RAY DIFFRACTION21(K 2 - K 141)
22X-RAY DIFFRACTION22(K 142 - K 264)
23X-RAY DIFFRACTION23(L 2 - L 141)
24X-RAY DIFFRACTION24(L 142 - L 264)
25X-RAY DIFFRACTION25(M 2 - M 141)
26X-RAY DIFFRACTION26(M 142 - M 264)
27X-RAY DIFFRACTION27(N 2 - N 141)
28X-RAY DIFFRACTION28(N 142 - N 264)
29X-RAY DIFFRACTION29(O 2 - O 141)
30X-RAY DIFFRACTION30(O 142 - O 264)
31X-RAY DIFFRACTION31(P 2 - P 141)
32X-RAY DIFFRACTION32(P 142 - P 264)
33X-RAY DIFFRACTION33(Q 2 - Q 141)
34X-RAY DIFFRACTION34(Q 142 - Q 264)
35X-RAY DIFFRACTION35(R 2 - R 141)
36X-RAY DIFFRACTION36(R 142 - R 264)
37X-RAY DIFFRACTION37(S 1 - S 137)
38X-RAY DIFFRACTION38(S 138 - S 298)
39X-RAY DIFFRACTION39(T 1 - T 137)
40X-RAY DIFFRACTION40(T 138 - T 298)
41X-RAY DIFFRACTION41(U 1 - U 137)
42X-RAY DIFFRACTION42(U 138 - U 298)
43X-RAY DIFFRACTION43(V 1 - V 137)
44X-RAY DIFFRACTION44(V 138 - V 298)
45X-RAY DIFFRACTION45(W 1 - W 137)
46X-RAY DIFFRACTION46(W 138 - W 298)
47X-RAY DIFFRACTION47(X 1 - X 137)
48X-RAY DIFFRACTION48(X 138 - X 298)
49X-RAY DIFFRACTION49(Y 1 - Y 237)
50X-RAY DIFFRACTION50(Y 238 - Y 315)
51X-RAY DIFFRACTION51(Y 316 - Y 372)
52X-RAY DIFFRACTION52(Z 1 - Z 237)
53X-RAY DIFFRACTION53(Z 238 - Z 315)
54X-RAY DIFFRACTION54(Z 316 - Z 372)
55X-RAY DIFFRACTION55(1 1 - 1 237)
56X-RAY DIFFRACTION56(1 238 - 1 315)
57X-RAY DIFFRACTION57(1 316 - 1 372)

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る