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- PDB-3prx: Structure of Complement C5 in Complex with CVF and SSL7 -

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基本情報

登録情報
データベース: PDB / ID: 3prx
タイトルStructure of Complement C5 in Complex with CVF and SSL7
要素
  • Cobra venom factor
  • Complement C5
  • Superantigen-like protein 7
キーワードIMMUNE SYSTEM/TOXIN / immune system / Complement / Staphylococcus aureus / IMMUNE SYSTEM-TOXIN complex
機能・相同性
機能・相同性情報


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / toxin activity / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / metal ion binding
類似検索 - 分子機能
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / : / Complement component 5, CUB domain / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / : / Complement component 5, CUB domain / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Enterotoxin / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Superantigen-like protein 7 / Complement C5 / Cobra venom factor
類似検索 - 構成要素
生物種Staphylococcus aureus (黄色ブドウ球菌)
Homo sapiens (ヒト)
Naja kaouthia (コブラ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.3 Å
データ登録者Laursen, N.S. / Andersen, G.R. / Sottrup-Jensen, L. / Andersen, K.R. / Spillner, E. / Braren, I.
引用ジャーナル: Embo J. / 年: 2011
タイトル: Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex.
著者: Laursen, N.S. / Andersen, K.R. / Braren, I. / Spillner, E. / Sottrup-Jensen, L. / Andersen, G.R.
履歴
登録2010年11月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02011年1月19日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年9月6日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Complement C5
B: Cobra venom factor
C: Complement C5
D: Cobra venom factor
X: Superantigen-like protein 7
Y: Superantigen-like protein 7
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)800,64612
ポリマ－798,5066
非ポリマー2,1406
水00
1
A: Complement C5
B: Cobra venom factor
X: Superantigen-like protein 7
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)400,3236
ポリマ－399,2533
非ポリマー1,0703
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Complement C5
D: Cobra venom factor
Y: Superantigen-like protein 7
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)400,3236
ポリマ－399,2533
非ポリマー1,0703
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)163.650, 181.960, 392.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resid 20:398 or resid 400:545)
211chain C and (resid 20:398 or resid 400:545)
112chain A and (resid 555:1625 or resid 2003)
212chain C and (resid 555:1625 or resid 2003)
113chain A and resid 1636:1680
213chain C and resid 1636:1680
114chain B and (resid 23:1473 or resid 2001:2004)
214chain D and (resid 23:1473 or resid 2001:2004)
115chain B and resid 1474:1498
215chain D and resid 1474:1498
116chain B and resid 1531:1604
216chain D and resid 1531:1604
117chain X
217chain Y

NCSアンサンブル:
ID
1
2
3
4
5
6
7

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要素

#1: タンパク質 Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 / Complement C5 beta chain / ...C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 / Complement C5 beta chain / Complement C5 alpha chain / C5a anaphylatoxin / Complement C5 alpha' chain


分子量: 188512.094 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P01031
#2: タンパク質 Cobra venom factor / CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / ...CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / Cobra venom factor beta chain


分子量: 184726.734 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Naja kaouthia (コブラ) / 参照: UniProt: Q91132
#3: タンパク質 Superantigen-like protein 7


分子量: 26014.383 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D3JIB2
#4: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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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: 3.66 Å3/Da / 溶媒含有率: 66.41 %
結晶化温度: 292 K / 手法: 蒸気拡散法 / pH: 7.4
詳細: 3 M sodium malonate, pH 7.4, VAPOR DIFFUSION, temperature 292K

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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: ESRF / ビームライン: ID29 / 波長: 0.9763
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2009年11月18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: 0.9763 Å / 相対比: 1
反射解像度: 4.3→49.214 Å / Num. obs: 77924 / % possible obs: 96.8 % / 冗長度: 5.1 % / Rsym value: 0.143 / Net I/σ(I): 11.4
反射 シェル最高解像度: 4.3 Å / 冗長度: 5.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.525 / % possible all: 98.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.6.4_486)精密化
XDSデータ削減
XSCALE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 ENTRIES 3KLS and 3HRZ

3kls

3hrz


解像度: 4.3→49.214 Å / SU ML: 0.62 / σ(F): 1.99 / 位相誤差: 24.12 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2614 1816 2.33 %
Rwork0.2078 --
obs0.2091 77924 96.86 %
溶媒の処理減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 160.973 Å2 / ksol: 0.346 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-22.7926 Å20 Å2-0 Å2
2--18.0864 Å2-0 Å2
3----40.879 Å2
精密化ステップサイクル: LAST / 解像度: 4.3→49.214 Å
タンパク質核酸リガンド溶媒全体
原子数48096 0 140 0 48236
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01251346
X-RAY DIFFRACTIONf_angle_d1.58466792
X-RAY DIFFRACTIONf_dihedral_angle_d26.29930370
X-RAY DIFFRACTIONf_chiral_restr0.0987642
X-RAY DIFFRACTIONf_plane_restr0.0078528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A4205X-RAY DIFFRACTIONPOSITIONAL
12C4205X-RAY DIFFRACTIONPOSITIONAL0.059
21A8177X-RAY DIFFRACTIONPOSITIONAL
22C8177X-RAY DIFFRACTIONPOSITIONAL0.104
31A335X-RAY DIFFRACTIONPOSITIONAL
32C335X-RAY DIFFRACTIONPOSITIONAL0.048
41B8319X-RAY DIFFRACTIONPOSITIONAL
42D8319X-RAY DIFFRACTIONPOSITIONAL0.045
51B173X-RAY DIFFRACTIONPOSITIONAL
52D173X-RAY DIFFRACTIONPOSITIONAL0.047
61B604X-RAY DIFFRACTIONPOSITIONAL
62D604X-RAY DIFFRACTIONPOSITIONAL0.048
71X1539X-RAY DIFFRACTIONPOSITIONAL
72Y1539X-RAY DIFFRACTIONPOSITIONAL0.045
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.41620.34571390.28825873X-RAY DIFFRACTION99
4.4162-4.54610.27171380.25285886X-RAY DIFFRACTION98
4.5461-4.69270.27161360.22385861X-RAY DIFFRACTION98
4.6927-4.86030.26011400.2025864X-RAY DIFFRACTION98
4.8603-5.05470.24691420.1955877X-RAY DIFFRACTION98
5.0547-5.28450.26371410.19185885X-RAY DIFFRACTION98
5.2845-5.56270.26951410.19545866X-RAY DIFFRACTION98
5.5627-5.91070.26341400.2225867X-RAY DIFFRACTION98
5.9107-6.36620.30491400.22835868X-RAY DIFFRACTION97
6.3662-7.00520.29021420.22855873X-RAY DIFFRACTION97
7.0052-8.01510.2611410.18295806X-RAY DIFFRACTION96
8.0151-10.08390.17641350.14945809X-RAY DIFFRACTION94
10.0839-49.21740.2711410.21985773X-RAY DIFFRACTION91
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)
12.5964-0.98950.39890.6440.10131.1682-0.20780.3338-0.1801-0.0664-0.05950.0932-0.7595-0.09250.22061.49540.7623-0.11021.6374-0.17261.13540.514349.4079-17.3478
21.18780.0817-0.8763-1.0137-0.45541.1036-0.7068-0.0663-0.0384-0.34830.3754-0.1765-0.25540.02990.37511.17310.2905-0.27170.4819-0.11411.00248.890854.6355-54.9777
31.13330.5019-0.24810.95031.81932.05540.26670.192-0.06470.0877-0.1506-0.48160.03950.16270.02361.5532-0.1251-0.19221.56880.23641.70941.1246.8263-60.6407
40.79330.8123-0.99171.614-0.83271.1563-0.3001-0.05050.60380.2287-0.1213-0.2845-0.48060.05310.34311.4273-0.0235-0.3911.12330.00851.385437.923538.9526-26.7459
51.01660.27090.60982.5248-0.01440.364-0.1658-0.1419-0.02350.14990.1803-0.0744-0.3608-0.2858-0.05491.43140.3369-0.09431.7250.00081.260217.368732.8677-17.3205
6-0.118-0.0706-0.01212.6079-2.46322.7885-0.3376-0.05870.1788-0.32670.1256-0.03810.4047-0.1840.14760.78560.0195-0.16870.8773-0.20120.88639.799331.7922-63.5881
75.553-0.60280.73660.8341-0.81541.867-0.17720.30680.31820.4773-0.20780.5302-0.28130.02940.37020.7773-0.064-0.07790.63560.03590.934721.683141.6537-89.2428
81.17611.0305-0.7822-0.1464-0.01791.24940.1149-0.03840.3336-0.22390.36410.8103-0.23490.0171-0.41211.70950.3449-0.18231.03710.07851.67762.299274.7139-63.4598
90.43-1.71811.81145.1914-1.10452.4832-0.07360.1779-0.08940.511-0.28390.23550.16760.7830.36041.411-0.0029-0.00541.56170.14681.321342.458750.1426-89.1353
103.74830.9731.36692.62052.49441.38260.05970.13730.13170.6213-0.0985-0.15270.2455-0.01950.01711.3101-0.2496-0.13991.01750.23381.22788.979656.8622-114.9019
11-0.3216-2.1366-1.4218-0.4363-1.60086.9853-0.08030.07640.037-0.2397-0.6803-0.1251-1.84790.08710.63481.70060.0875-0.13261.3552-0.29481.332817.802147.7073-29.602
120.6481-1.6741-0.05081.47550.17791.0433-0.4956-0.0397-0.66070.16190.13620.6073-0.24290.10920.18761.68910.40730.42551.13980.21161.3522130.7055-77.0825-80.5371
131.7986-1.47040.22091.33530.25072.36050.56040.22850.6741-0.1052-0.5775-0.28080.24370.28340.0581.08320.16740.11041.16990.34971.3267132.3087-75.5059-41.705
140.67842.712-0.56313.6343-0.29282.8561-0.19790.22180.57460.39740.2320.22970.05370.3002-0.03981.030.0115-0.24561.09080.16481.5686125.0315-44.3805-31.2576
150.53630.15060.33180.55380.15342.33640.4139-0.10650.5816-0.04390.0942-1.0112-0.1670.5952-0.41570.9437-0.15890.09571.19550.3581.63120.6172-41.3483-65.7884
162.3133-1.1275-0.13312.77-3.04253.0549-0.1005-0.18070.1616-0.54320.2445-0.57240.3628-0.4221-0.08331.177-0.04350.07481.08340.11411.1948114.826-59.6535-79.1939
170.1463-0.7008-0.11652.9818-0.25711.2953-0.00860.04460.0536-0.1092-0.3942-0.38580.15760.0290.24050.938-0.13030.06830.90440.14231.1172108.7422-74.9455-35.2907
181.98221.12780.19122.1050.82111.2884-0.26550.0501-0.44060.2867-0.18170.04650.02240.0330.32530.97070.0681-0.03520.88690.09731.0939116.2884-68.1247-7.1265
191.6429-0.97970.43461.129-0.470.99270.4536-0.3268-0.6902-0.3218-0.231-0.10830.0569-0.001-0.27411.15310.2729-0.00721.22590.12991.5459151.1847-84.439-32.6333
202.5097-0.69460.4852-0.3885-0.34470.7902-0.39010.0815-0.10950.26730.194-0.195-0.31410.05560.21051.30.074-0.13431.06380.09621.3955125.4203-48.0835-2.7832
215.06231.3063-1.98654.0797-1.39821.52580.0329-0.1321-0.11230.8339-0.26290.0317-0.1477-0.01180.14811.2744-0.1143-0.06590.98950.00831.0693131.4673-84.807318.3571
220.1773-0.1169-1.5139-0.4626-0.50014.9103-0.5677-0.3478-0.24890.0412-0.09680.083-0.01411.06640.48981.1520.11370.20361.33380.09981.2128128.3309-62.0756-65.6798
230.0252-0.2041-1.76712.7007-0.81782.57290.0253-0.17950.0227-0.1006-0.0686-0.1380.1943-0.11280.02050.83750.1462-0.13841.1104-0.00960.888252.9726-0.4484-17.5062
241.50612.99361.45971.627-0.27863.1089-0.8182-0.07770.5061-0.04780.27530.3969-0.05740.03370.42810.82450.1643-0.06360.7458-0.19351.007839.2785-9.1028-52.0338
250.71942.4581-2.1120.3419-0.70282.3466-0.39780.1728-0.5327-0.001-0.407-0.4021-0.0734-1.03080.60431.07410.0982-0.23541.6527-0.05321.47982.5304-6.0247-55.7568
26-0.5908-1.0248-0.34891.3412-0.03811.64250.02670.3801-0.2832-0.0302-0.35290.5956-0.0407-0.61510.26570.9991-0.0811-0.0771.5904-0.07961.405612.981910.0384-22.8144
27-1.3908-0.5576-0.15971.3733-1.26722.1158-0.4394-0.1751-0.34480.0607-0.0349-0.8072-0.04490.03910.39050.5840.0962-0.06890.8453-0.04520.955437.027516.9329-18.3938
281.09151.22340.3623-0.975-0.61130.5897-0.11790.07090.71410.9181-0.21620.0957-0.6305-0.02670.39991.0801-0.0974-0.36960.36160.17571.11136.13239.6485-60.5199
291.74650.28710.18781.33930.26920.25520.73150.9265-0.04840.0004-0.108-0.6495-0.0467-0.2194-0.52920.38090.2832-0.0130.8493-0.04360.803620.86418.0102-89.6477
302.1592-2.21520.62851.73-0.4362.45010.1033-0.96010.2042-0.1037-0.2577-0.11830.23740.01240.08630.9974-0.035-0.00411.2862-0.12510.997151.7216-21.2159-96.4636
311.92580.2523-1.61494.19470.66231.14960.19280.32370.1077-0.0208-0.36560.5354-0.012-0.10450.14540.61290.087-0.07080.7714-0.05160.726742.7194-37.19-74.1217
320.7458-0.767-0.3012.5379-1.09662.352-0.304-0.5193-0.1314-0.07530.53620.16670.0259-0.7432-0.2060.54990.0931-0.04391.054-0.26591.061317.3327-26.1785-87.3589
332.42311.3485-1.30691.42181.182.2984-00.3103-0.6279-0.1686-0.20580.0171-0.3442-0.3050.12590.71390.1794-0.00321.70670.05070.934526.8692-12.0117-124.8944
34-0.13860.27970.22951.07620.59540.6074-0.00510.80090.33050.13820.2249-0.66160.1603-0.3763-0.33011.10770.13660.29331.5075-0.15151.31251.5003-29.7204-64.7421
350.29852.52262.43490.5014-0.14123.48480.07960.44520.13470.0771-0.61160.30940.8410.50120.46850.99210.13570.14261.2556-0.19991.196932.56491.1504-29.8443
363.80510.4443-1.7575-0.0791-0.96971.65430.05820.02620.2712-0.02770.363-0.00140.6062-0.5059-0.35940.76310.13810.06620.93730.21950.616283.6578-22.2517-74.6034
371.31892.57212.3831.2568-1.59172.05710.15150.28360.1745-0.0401-0.3231-0.0762-0.0536-0.28870.12910.73020.15890.13190.927801.153770.6025-41.9028-44.6444
380.91451.78240.1405-0.71291.42112.9192-0.1560.0245-0.01750.2812-0.2580.2582-0.2772-0.04010.39311.42220.14330.11811.05690.14511.654471.4523-78.8023-48.2815
391.9549-1.82820.53380.4155-1.080.9065-0.0573-0.2605-0.13680.0312-0.38540.3558-0.03930.53060.3491.2741-0.07870.06491.3816-0.09341.37991.5254-63.1328-76.64
401.54860.33020.1480.00990.31262.7084-0.1411-0.08560.07-0.2116-0.22050.1652-0.2930.07890.29650.8641-0.0015-0.05940.65-0.00561.00499.9635-39.2201-75.3492
410.09731.9918-0.73852.5096-0.55781.9587-0.1994-0.0144-0.56150.0554-0.0639-0.7127-0.00890.38540.27920.5496-0.0093-0.13881.32460.33290.907987.9896-47.5355-35.3399
421.3995-0.10040.1549-0.58910.52560.23520.16590.10650.07510.24860.2421-0.0504-0.2327-0.0036-0.32160.6291-0.01310.2110.40680.17850.805482.3687-67.7993-10.0534
431.243-0.3647-2.02743.1152-0.0226-0.901-0.3736-0.7376-0.007-0.44520.18980.07920.00580.40120.05011.09440.00690.01691.217-0.02830.934453.6592-37.1127-0.7649
445.2369-0.0357-0.60262.15942.08862.194-0.23940.2156-0.54930.19990.1282-0.01430.15990.17250.10020.62540.02320.05390.62340.05920.67340.1205-40.9047-25.9955
451.93-0.95061.16760.3422-2.74942.69460.261-0.0656-0.4949-0.2929-0.10560.38380.8864-0.1299-0.04831.1532-0.00670.29250.8114-0.00341.393948.5833-68.8911-16.701
461.91680.6029-1.9153.3667-3.23811.70740.0328-0.5583-0.13920.9639-0.12130.2752-1.06310.66440.07742.0365-0.05050.0461.52830.05081.372858.3632-67.128823.1659
470.4674-0.3047-0.41431.95290.48630.70920.0997-0.07380.56-0.22080.4464-0.32670.1705-0.0959-0.37041.4308-0.06050.08651.3487-0.24591.645147.1901-80.0471-42.154
48-1.95282.97121.00550.4732-4.12128.5416-1.25660.36540.03070.19460.1121-0.637-0.5095-2.59530.91720.3897-0.0401-0.02671.1027-0.05910.908283.04-44.8769-66.8824
493.87560.5661.41930.87960.462-0.2696-0.29862.6299-0.49120.15220.29380.1478-0.0778-0.4538-0.02521.7523-0.26460.47852.74320.26051.947875.504625.1934-43.9955
500.7554-0.83021.45850.98870.60383.5795-0.4815-0.08130.8082-0.18670.13410.15820.03870.99870.22620.7673-0.1227-0.04031.53070.16311.331362.991218.7416-29.291
512.0195-0.3845-1.33350.50331.02773.20750.0906-0.52160.48340.3058-0.5508-0.17690.8115-0.59530.30661.3268-0.04290.09351.6191-0.35791.2245107.394-6.9421-41.8957
520.6783-0.63970.00422.0049-1.35491.26670.3122-0.09-0.02090.1556-0.22120.14290.15720.0318-0.04690.9939-0.2375-0.02110.90730.01511.1576101.8273-16.0857-59.2296
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESID 23:125 AND CHAIN B
2X-RAY DIFFRACTION2(RESID 126:220 OR RESID 2001:2002) AND CHAIN B
3X-RAY DIFFRACTION3RESID 221:340 AND CHAIN B
4X-RAY DIFFRACTION4RESID 341:437 AND CHAIN B
5X-RAY DIFFRACTION5RESID 438:542 AND CHAIN B
6X-RAY DIFFRACTION6(RESID 543:582 OR RESID 733:812) AND CHAIN B
7X-RAY DIFFRACTION7RESID 813:917 AND CHAIN B
8X-RAY DIFFRACTION8(RESID 918:969 OR RESID 1270:1333) AND CHAIN B
9X-RAY DIFFRACTION9(RESID 1334:1473 OR RESID 2003:2004) AND CHAIN B
10X-RAY DIFFRACTION10RESID 1474:1642 AND CHAIN B
11X-RAY DIFFRACTION11RESID 583:649 AND CHAIN B
12X-RAY DIFFRACTION12RESID 23:125 AND CHAIN D
13X-RAY DIFFRACTION13(RESID 126:220 OR RESID 2001:2002) AND CHAIN D
14X-RAY DIFFRACTION14RESID 221:340 AND CHAIN D
15X-RAY DIFFRACTION15RESID 341:437 AND CHAIN D
16X-RAY DIFFRACTION16RESID 438:542 AND CHAIN D
17X-RAY DIFFRACTION17(RESID 543:582 OR RESID 733:812) AND CHAIN D
18X-RAY DIFFRACTION18RESID 813:917 AND CHAIN D
19X-RAY DIFFRACTION19(RESID 918:969 OR RESID 1270:1333) AND CHAIN D
20X-RAY DIFFRACTION20(RESID 1334:1473 OR RESID 2003:2004) AND CHAIN D
21X-RAY DIFFRACTION21RESID 1474:1642 AND CHAIN D
22X-RAY DIFFRACTION22RESID 583:649 AND CHAIN D
23X-RAY DIFFRACTION23RESID 19:120 AND CHAIN A
24X-RAY DIFFRACTION24RESID 121:224 AND CHAIN A
25X-RAY DIFFRACTION25RESID 225:349 AND CHAIN A
26X-RAY DIFFRACTION26RESID 350:460 AND CHAIN A
27X-RAY DIFFRACTION27RESID 461:566 AND CHAIN A
28X-RAY DIFFRACTION28(RESID 567:606 OR RESID 760:821) AND CHAIN A
29X-RAY DIFFRACTION29(RESID 822:930 OR RESID 2003) AND CHAIN A
30X-RAY DIFFRACTION30(RESID 931:983 OR RESID 1305:1367) AND CHAIN A
31X-RAY DIFFRACTION31RESID 984:1304 AND CHAIN A
32X-RAY DIFFRACTION32RESID 1368:1514 AND CHAIN A
33X-RAY DIFFRACTION33RESID 1525:1676 AND CHAIN A
34X-RAY DIFFRACTION34(RESID 676:759 ) AND CHAIN A
35X-RAY DIFFRACTION35RESID 607:673 AND CHAIN A
36X-RAY DIFFRACTION36RESID 19:120 AND CHAIN C
37X-RAY DIFFRACTION37RESID 121:224 AND CHAIN C
38X-RAY DIFFRACTION38RESID 225:349 AND CHAIN C
39X-RAY DIFFRACTION39RESID 350:460 AND CHAIN C
40X-RAY DIFFRACTION40RESID 461:566 AND CHAIN C
41X-RAY DIFFRACTION41(RESID 567:606 OR RESID 760:821) AND CHAIN C
42X-RAY DIFFRACTION42(RESID 822:930 OR RESID 2003) AND CHAIN C
43X-RAY DIFFRACTION43(RESID 931:983 OR RESID 1305:1367) AND CHAIN C
44X-RAY DIFFRACTION44RESID 984:1304 AND CHAIN C
45X-RAY DIFFRACTION45RESID 1368:1514 AND CHAIN C
46X-RAY DIFFRACTION46RESID 1525:1676 AND CHAIN C
47X-RAY DIFFRACTION47(RESID 676:759 ) AND CHAIN C
48X-RAY DIFFRACTION48RESID 607:673 AND CHAIN C
49X-RAY DIFFRACTION49RESID 40:130 AND CHAIN X
50X-RAY DIFFRACTION50RESID 131:231 AND CHAIN X
51X-RAY DIFFRACTION51RESID 40:130 AND CHAIN Y
52X-RAY DIFFRACTION52RESID 131:231 AND CHAIN Y

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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

-
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