[日本語] English
万見
- PDB-3csy: Crystal structure of the trimeric prefusion Ebola virus glycoprot... -

+
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: 3csy
タイトルCrystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor
要素
  • (Envelope glycoprotein ...) x 2
  • Fab KZ52 heavy chain
  • Fab KZ52 light chain
キーワードIMMUNE SYSTEM/VIRAL PROTEIN / glycoprotein-antibody complex / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
機能・相同性
機能・相同性情報


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane
類似検索 - 分子機能
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Envelope glycoprotein / Envelope glycoprotein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Ebola virus - Mayinga (エボラウイルス)
Zaire
1976
手法X線回折 / シンクロトロン / phase combination of model phases from an independently solved Fab KZ52, Fab KZ52 selenium anomalous signal / 分子置換 / 解像度: 3.4 Å
データ登録者Lee, J.E. / Fusco, M.L. / Hessell, A.J. / Oswald, W.B. / Burton, D.R. / Saphire, E.O.
引用ジャーナル: Nature / 年: 2008
タイトル: Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor.
著者: Lee, J.E. / Fusco, M.L. / Hessell, A.J. / Oswald, W.B. / Burton, D.R. / Saphire, E.O.
履歴
登録2008年4月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02008年7月8日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Non-polymer description / Version format compliance
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12021年3月31日Group: Source and taxonomy / Structure summary / カテゴリ: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain
改定 2.22021年10月20日Group: Database references / Derived calculations
カテゴリ: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands

-
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
A: Fab KZ52 heavy chain
B: Fab KZ52 light chain
C: Fab KZ52 heavy chain
D: Fab KZ52 light chain
E: Fab KZ52 heavy chain
F: Fab KZ52 light chain
G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
I: Envelope glycoprotein GP1
J: Envelope glycoprotein GP2
K: Envelope glycoprotein GP1
L: Envelope glycoprotein GP2
M: Envelope glycoprotein GP1
N: Envelope glycoprotein GP2
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)406,07124
ポリマ－399,83716
非ポリマー6,2348
水00
1
A: Fab KZ52 heavy chain
B: Fab KZ52 light chain
C: Fab KZ52 heavy chain
D: Fab KZ52 light chain
E: Fab KZ52 heavy chain
F: Fab KZ52 light chain
I: Envelope glycoprotein GP1
J: Envelope glycoprotein GP2
K: Envelope glycoprotein GP1
L: Envelope glycoprotein GP2
M: Envelope glycoprotein GP1
N: Envelope glycoprotein GP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)304,41118
ポリマ－299,87812
非ポリマー4,5336
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area45840 Å2
ΔGint-161 kcal/mol
Surface area97630 Å2
手法PISA
2
G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
ヘテロ分子

G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
ヘテロ分子

G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)304,97918
ポリマ－299,87812
非ポリマー5,1026
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area46200 Å2
ΔGint-150 kcal/mol
Surface area96470 Å2
手法PISA
単位格子
Length a, b, c (Å)273.710, 273.710, 409.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
要素

-
Envelope glycoprotein ... , 2種, 8分子 IKMOJLNP

#3: タンパク質
Envelope glycoprotein GP1


分子量: 37027.480 Da / 分子数: 4 / 断片: deletion of residues 312-463 / Mutation: T42V, T230V / 由来タイプ: 組換発現
詳細: Weak or discontinuous electron density is observed in the outer regions of the glycoprotein (residues 268-278 and 299-310) and these residues are tentatively assigned
由来: (組換発現) Ebola virus - Mayinga, Zaire, 1976 (エボラウイルス)
株: Mayinga-76 / 遺伝子: GP / 細胞株 (発現宿主): HEK293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q05320
#4: タンパク質
Envelope glycoprotein GP2


分子量: 14779.716 Da / 分子数: 4 / 断片: deletion of residues 633-676 / 由来タイプ: 組換発現
由来: (組換発現) Ebola virus - Mayinga, Zaire, 1976 (エボラウイルス)
株: Mayinga-76 / 遺伝子: GP / 細胞株 (発現宿主): HEK293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P87666, UniProt: Q05320*PLUS

-
抗体 , 2種, 8分子 ACEGBDFH

#1: 抗体
Fab KZ52 heavy chain


分子量: 24208.557 Da / 分子数: 4 / 断片: heavy chain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
解説: The antibody was identified from a human survivor of the 1995 Kikwit, Zaire Ebola virus outbreak
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
株 (発現宿主): CHO-K1
#2: 抗体
Fab KZ52 light chain


分子量: 23943.453 Da / 分子数: 4 / 断片: light chain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
解説: The antibody was identified from a human survivor of the 1995 Kikwit, Zaire Ebola virus outbreak
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
株 (発現宿主): CHO-K1

-
糖 , 4種, 8分子

#5: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1114.016 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

-
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: 3.69 Å3/Da / 溶媒含有率: 66.67 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 8.5% (w/v) PEG 10,000, 0.1 M Tris-HCl pH 8.5, 0.4 M sodium acetate, 10% (v/v) PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
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: ALS / ビームライン: 5.0.2 / 波長: 0.9803 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2006年8月23日
放射モノクロメーター: Double crystal, Si(111) / 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: 0.9803 Å / 相対比: 1
反射解像度: 3.4→48.37 Å / Num. obs: 151305 / % possible obs: 96.2 % / 冗長度: 4.14 % / Rmerge(I) obs: 0.142 / Χ2: 0.94 / Net I/σ(I): 6.2 / Scaling rejects: 19362
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
3.4-3.523.580.5681.754223148671.1494.7
3.52-3.663.640.507256023149431.1294.6
3.66-3.833.740.4582.357498148191.194.6
3.83-4.033.860.3892.759051148361.0894.2
4.03-4.283.930.2783.659880147701.0294
4.28-4.613.950.1974.761267150410.9495.6
4.61-5.084.230.157667624154120.9398
5.08-5.814.670.1456.775917157020.8899.8
5.81-7.324.780.1058.977102156620.899.6
7.32-48.374.90.04718.576813152530.6196.8

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類NB
d*TREK9.6Dデータスケーリング
PHASER位相決定
直接法位相決定
PHENIX精密化
PDB_EXTRACT3.005データ抽出
BOSデータ収集
d*TREKデータ削減
SHARP位相決定
精密化構造決定の手法: phase combination of model phases from an independently solved Fab KZ52, Fab KZ52 selenium anomalous signal
解像度: 3.4→48.369 Å / 交差検証法: THROUGHOUT / σ(F): 0.02 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.302 4405 3 %random
Rwork0.261 ---
obs0.263 146996 93.44 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 65.699 Å2 / ksol: 0.333 e/Å3
原子変位パラメータBiso max: 65.22 Å2 / Biso mean: 115.8 Å2 / Biso min: 240.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.338 Å2-0 Å20 Å2
2--1.338 Å20 Å2
3----2.677 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å / Luzzati sigma a obs: 0.97 Å
精密化ステップサイクル: LAST / 解像度: 3.4→48.369 Å
タンパク質核酸リガンド溶媒全体
原子数23122 0 417 0 23539
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01146668
X-RAY DIFFRACTIONf_angle_d1.183956
X-RAY DIFFRACTIONf_chiral_restr0.063760
X-RAY DIFFRACTIONf_plane_restr0.0057314
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.4390.4561180.4074557467588
3.439-3.4790.3931290.3924533466289
3.479-3.5220.3831140.384507462190
3.522-3.5660.3571460.3744518466489
3.566-3.6130.3611410.3484592473390
3.613-3.6620.3741310.3524585471689
3.662-3.7150.3871510.3474588473991
3.715-3.770.3481460.3424496464290
3.77-3.8290.4271420.3344610475290
3.829-3.8920.3271590.3144580473990
3.892-3.9590.3161680.3044572474090
3.959-4.0310.321500.2974587473791
4.031-4.1080.331210.2844590471190
4.108-4.1920.2721620.2684669483192
4.192-4.2830.3161640.2624612477692
4.283-4.3830.3441530.2434697485093
4.383-4.4920.2831420.2294760490293
4.492-4.6140.231590.2234771493094
4.614-4.7490.2551420.2234854499695
4.749-4.9030.2621250.2174922504797
4.903-5.0780.2821650.2254996516198
5.078-5.2810.3011300.235005513599
5.281-5.5210.2821460.235055520199
5.521-5.8110.3111510.2315079523099
5.811-6.1750.3261620.2425018518099
6.175-6.650.2981640.2325034519899
6.65-7.3180.2911550.2295046520199
7.318-8.3720.2951450.1974974511998
8.372-10.530.1781790.1554964514398
10.53-48.3740.2771450.2424820496595
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)
1-0.01982.25150.97335.89080.99362.86490.02470.1147-0.16570.1984-0.20640.05660.223-0.09530.00010.6808-0.05620.02160.7412-0.03650.8338128.7742-96.2638-187.508
21.71610.0265-3.31883.1041-2.64854.30390.0697-0.3127-0.2029-0.0543-0.3588-0.19330.25780.331900.8940.0231-0.02540.910.05280.9332181.7777-120.2717-250.0211
33.7947-3.12821.02214.2746-0.50450.65540.14220.1603-0.16250.117-0.09220.16620.26410.071900.931-0.0414-0.09420.9944-0.06140.851396.9607-121.8991-262.471
41.80762.8751-0.26053.8174-1.97732.42650.03580.34050.0905-0.10560.0611-0.3254-0.0041-0.2704-00.85160.0386-0.09591.03270.01550.981389.9914-95.3477-280.9975
52.29441.3069-0.51851.3552.40092.83820.792-1.928-0.87691.1833-1.1964-0.61870.38020.0584-0.00011.5877-0.4572-0.12651.83340.38821.5702124.8446-94.8569-154.6656
60.9392-0.9444-1.53660.5621-0.2180.84790.24680.0415-0.6097-0.052-0.1814-0.49060.67310.4633-01.52930.2971-0.28981.3921-0.06621.7064211.3676-133.5396-258.5579
72.464-1.09240.8851.57090.10731.12720.2517-0.0894-0.61540.418-0.18640.22020.6004-0.351601.3961-0.2041-0.00031.2629-0.17381.17870.8993-136.6581-277.1601
81.35761.48530.38970.5279-1.877-0.48660.16660.4752-0.2237-0.69410.16910.38410.6555-0.88701.6464-0.112-0.36161.8340.07171.495559.3594-106.9302-289.9713
95.58610.4535-1.89982.33932.83324.66430.05680.0891-0.10980.4527-0.39210.84130.3002-0.910600.8795-0.23140.06681.0088-0.15871.1297109.9111-107.6098-185.0618
105.7775-0.98341.16861.4881.30753.9790.2802-0.91260.24510.0965-0.2958-0.51610.34490.7207-01.2359-0.0408-0.09011.24860.06721.0744189.7508-126.0151-230.1693
114.0801-0.22561.32980.91081.98154.59350.50870.6397-0.4618-0.2613-0.01860.02650.47020.3789-0.00011.10910.1608-0.10321.2785-0.14221.1779107.0689-138.6035-272.8723
124.6362-1.46440.27982.9466-0.58220.87820.22720.14340.7186-0.1480.08110.2372-0.3252-0.375-01.14230.05760.04521.12720.17841.185782.3722-78.3071-292.8916
130.3108-0.8568-1.08821.0804-0.59322.16330.6518-1.38920.47110.7806-0.84560.2718-0.1677-0.4722-0.00011.4992-0.41720.24482.0592-0.38431.8116109.5918-91.2436-151.8155
141.37990.09950.80721.9639-0.177-0.01050.34940.4605-0.0580.342-0.0707-0.1706-0.03150.1729-01.30460.1461-0.10221.79050.11471.5524221.7505-126.419-248.6445
151.96721.12411.23173.6914-0.3031.94930.00090.6779-0.30010.0693-0.1917-0.05640.45090.38080.00011.15360.1007-0.14971.6185-0.25841.015774.8678-139.7705-292.2048
160.40741.57420.99671.28710.77430.67640.6306-0.71020.219-0.15060.18771.50510.4848-0.74930.00031.51130.0176-0.00441.91480.60682.218848.968-95.2205-287.4831
17-0.07480.3028-0.22051.07370.50130.29390.37340.5281-1.0332-0.65120.35870.2508-0.37850.0731-00.97780.0841-0.19350.8564-0.01310.901130.4378-118.1736-201.4759
187.5785-7.403-6.59768.81534.64213.22070.7346-2.57964.0332-0.09221.7092-1.2007-1.46190.17890.27731.39480.1875-0.07481.3621-0.0071.239157.6645-129.0919-212.831
190.53920.2485-0.356-0.69632.2316-1.2701-0.3252-0.15980.10210.525-0.0695-0.15840.61890.01430.0011.15110.0095-0.17120.8942-0.00481.2322146.1736-126.0971-204.6469
204.18510.27550.3078-0.249-0.3223-0.2227-0.6386-3.09113.39911.1205-1.04810.34840.4256-0.166-0.09320.760.14870.14530.81540.18350.526126.8402-115.3571-204.9236
210.0884-0.1839-0.13281.3069-0.36270.6601-0.45640.7745-0.6269-0.39340.49370.05040.46870.1713-0.00010.929-0.047-0.12470.9125-0.02340.8935125.1622-129.5889-219.3034
220.4842-0.0192-0.39050.27840.33090.7134-0.1644-0.98990.6585-0.63291.51421.361-0.475-2.114-0.00061.2584-0.08240.13731.00550.08590.9937130.1069-115.4077-228.9853
231.97940.16120.21241.5359-0.886-0.5716-0.4763-0.2575-0.23520.11560.12770.3550.39810.1221-0.00021.0401-0.0488-0.03911.01850.1160.865112.8523-133.1564-243.0679
243.1847-0.88027.15811.7266-2.58321.9943-1.29770.3001-0.3098-0.5987-0.5735-0.6306-3.6973-3.868-0.16391.2237-0.16410.08691.45430.05020.9969112.2417-128.8076-212.9041
25-0.2097-0.1440.156-1.6218-0.40470.08980.92890.24880.49070.66820.10130.2664-0.26480.5027-0.00151.2226-0.07680.08391.23920.05841.2858110.0224-133.2785-227.9412
26-0.2124-0.07670.27510.2517-0.1040.01581.05192.74451.1286-0.5364-0.63470.62220.4012-2.00280.00110.9551-0.2491-0.06241.1729-0.33110.754117.1526-130.8705-248.8089
270.90280.1539-0.30430.3918-0.47190.03450.0496-0.8348-0.1777-0.07890.2853-0.88670.58670.20650.00020.9198-0.1150.06191.0563-0.16231.0937133.6-136.7435-238.2139
280.19680.05990.2430.19620.09740.44410.03881.8305-0.4222-1.7704-0.7944-0.0822-1.169-0.2722-0.00241.1085-0.0327-0.21141.0471-0.05990.943135.2544-119.5401-237.7493
290.990.047-0.08430.2452-2.63580.00630.1002-0.39790.11370.44750.02290.04530.9361-0.15560.00030.9677-0.0774-0.01340.8388-0.16490.9961161.7005-132.3847-237.2762
30-0.25190.04030.08660.23010.09050.0421.25041.94142.5061-0.04441.8836-0.53281.22011.8926-0.0011.5377-0.0004-0.04851.1877-0.21521.0071134.8696-143.0281-250.9134
310.34030.31410.1205-0.5737-1.3613-0.20820.4059-0.3071-1.0449-0.9534-0.7328-0.5048-0.5867-0.26690.00051.3476-0.05330.17040.8875-0.2851.0819149.447-141.0693-245.2065
32-0.02120.03710.29550.133-0.1864-0.11640.1560.2477-0.5655-0.56570.66-0.098-1.29013.27540.00310.7555-0.0116-0.18330.8876-0.1540.8068162.5825-127.1227-233.9961
330.4101-0.016-1.7371.12850.37040.89050.2296-0.8063-0.30730.5144-0.46250.45150.2688-0.80880.00061.04950.1068-0.05570.7995-0.11990.6734146.8818-131.142-221.6408
340.4784-0.00830.17380.30260.07760.20260.7007-0.07740.3111.3976-1.0513-1.3747-1.6317-0.11310.00061.1463-0.0595-0.02821.2741-0.19060.8355141.4699-116.2302-229.006
350.0833-0.10610.0518-0.3373-0.5115-0.24220.39070.333-0.2154-1.04060.0497-0.15530.29830.2673-0.00040.90670.18170.00021.2683-0.22031.3108109.7196-88.5157-297.5957
36-0.0524-0.148-0.08250.06180.03640.2089-1.6682-2.2399-1.2480.4073-0.11411.26091.98970.9308-0.00121.4955-0.1463-0.17221.1695-0.05291.1486136.3162-105.9772-303.685
370.7164-0.78860.3107-0.1607-1.16-0.1229-0.15911.07710.03110.0113-0.07130.41810.2544-0.56780.0011.2076-0.13370.06710.8812-0.07851.3061121.7145-99.2598-302.8852
380.0789-0.4436-0.01190.27730.38440.1117-0.4190.67-1.32482.5630.47963.3109-0.0749-0.9837-0.00240.75620.1429-0.0860.9246-0.21971.0772109.491-83.4144-293.3346
390.070.7237-0.14620.6050.40470.3607-0.08680.8613-0.14130.1043-0.6195-0.1110.29340.328301.1158-0.0369-0.01550.7533-0.0551.0633125.345-73.6442-301.8608
400.1482-0.19310.3625-0.1213-0.00890.3101-0.2934-1.85230.31040.41720.51372.4888-1.611-0.38080.00010.8777-0.1754-0.06461.12060.04581.2645131.3-75.8731-285.4859
413.0588-1.17470.25762.45461.06941.91650.05680.48280.1082-0.27020.3495-0.2016-0.28710.0805-0.00020.8425-0.0018-0.11480.7937-0.07390.8369128.1302-120.0333-209.5926
421.52060.1561-0.66511.6583-0.71394.8983-0.1469-0.3169-0.59210.1036-0.0076-0.37130.5589-0.10670.00010.9299-0.0495-0.02840.80120.08990.963128.6212-137.8083-204.0036
431.81320.0195-2.08121.25830.10731.6576-0.0744-0.4849-0.7832-0.07340.2546-0.010.37820.1019-0.00021.24520.0461-0.00921.02650.19160.993129.8622-142.3969-181.8504
440.82630.33290.52020.2385-0.57941.27561.2091-0.3099-0.1490.8367-2.2747-1.48470.5685-0.1063-0.00211.2962-0.0661-0.01530.5547-0.09991.0387126.1694-146.2603-174.9323
451.7435-0.4635-0.21931.07090.96333.4793-0.3756-0.07920.4586-0.4680.53540.0419-0.32210.1510.00020.8601-0.0819-0.14421.2287-0.00030.8658121.612-132.1937-243.8674
462.77831.31410.59413.5576-0.43751.5590.0849-0.0338-0.60530.3217-0.22930.28160.4927-0.4046-0.00011.194-0.1551-0.03580.9476-0.09410.9243121.0592-149.2132-236.2021
470.87470.19920.23530.27360.81280.2007-0.253-0.5396-0.70230.7846-0.1272-0.11420.2919-0.79340.00031.5143-0.3926-0.22791.4444-0.09761.6521102.986-162.5207-239.7395
480.4354-0.1505-0.2551-0.2010.05940.3393-0.413-0.226-0.83151.1655-0.341.00120.14010.047-0.00121.599-0.0128-0.40481.28510.1811.5072100.5819-171.2033-242.1005
493.62451.9132-0.4570.2324-0.04872.0406-0.02130.31680.89630.39030.0232-0.3057-0.4183-0.34750.00011.0692-0.0715-0.05580.8669-0.15290.8472156.5489-129.0055-231.4226
503.1287-0.1052-0.45863.0189-0.24071.50680.04050.0964-0.3783-0.05030.0509-0.06860.60780.006-0.00011.09240.0617-0.07580.7918-0.07940.951154.8026-146.5762-225.5654
511.4577-0.37420.50841.0121-1.3431.0992-0.21770.1072-0.2624-0.12430.5582-0.52860.57340.0044-0.00021.37710.10670.14260.9585-0.18691.3062170.4866-161.9418-231.3648
520.2519-0.9336-0.01710.256-0.0390.4627-1.05390.72890.3535-0.86391.09630.84951.42730.42080.00151.1825-0.23610.20160.92650.06631.1473176.2528-168.2916-228.1748
533.0215-1.7434-1.19961.5724-0.04760.0738-0.0983-0.4504-0.17820.1420.0621-0.2683-0.2927-0.1786-0.00010.9992-0.12040.04230.8946-0.07341.1904115.514-81.841-296.1242
542.21320.290.21181.5357-0.20212.667-0.04550.48350.2058-0.75780.20450.23970.211-0.171101.0872-0.0235-0.17951.2173-0.00451.1163116.6417-82.5362-314.8001
551.5644-0.31290.2223-0.2530.10790.74050.10890.6325-1.2323-0.85960.0825-0.3829-0.27890.010701.4236-0.016-0.21371.78780.09861.5275100.3207-93.024-326.7007
560.06140.0346-0.1506-0.1791-0.1055-0.0607-0.1149-0.35811.7057-1.22890.74450.72561.1152-1.06150.00190.848-0.00720.07652.16360.17291.214892.084-89.6662-331.4657
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2C1 - 119
3X-RAY DIFFRACTION3E1 - 119
4X-RAY DIFFRACTION4G1 - 119
5X-RAY DIFFRACTION5A120 - 228
6X-RAY DIFFRACTION6C120 - 228
7X-RAY DIFFRACTION7E120 - 228
8X-RAY DIFFRACTION8G120 - 228
9X-RAY DIFFRACTION9B1 - 111
10X-RAY DIFFRACTION10D1 - 111
11X-RAY DIFFRACTION11F1 - 111
12X-RAY DIFFRACTION12H1 - 111
13X-RAY DIFFRACTION13B112 - 211
14X-RAY DIFFRACTION14D112 - 211
15X-RAY DIFFRACTION15F112 - 211
16X-RAY DIFFRACTION16H112 - 211
17X-RAY DIFFRACTION17J502 - 520
18X-RAY DIFFRACTION18J523 - 533
19X-RAY DIFFRACTION19J534 - 551
20X-RAY DIFFRACTION20J552 - 564
21X-RAY DIFFRACTION21J565 - 585
22X-RAY DIFFRACTION22J586 - 599
23X-RAY DIFFRACTION23L503 - 522
24X-RAY DIFFRACTION24L525 - 533
25X-RAY DIFFRACTION25L534 - 551
26X-RAY DIFFRACTION26L552 - 564
27X-RAY DIFFRACTION27L565 - 585
28X-RAY DIFFRACTION28L586 - 597
29X-RAY DIFFRACTION29N502 - 521
30X-RAY DIFFRACTION30N524 - 533
31X-RAY DIFFRACTION31N534 - 551
32X-RAY DIFFRACTION32N552 - 564
33X-RAY DIFFRACTION33N565 - 585
34X-RAY DIFFRACTION34N586 - 599
35X-RAY DIFFRACTION35P503 - 521
36X-RAY DIFFRACTION36P525 - 533
37X-RAY DIFFRACTION37P534 - 551
38X-RAY DIFFRACTION38P552 - 564
39X-RAY DIFFRACTION39P565 - 585
40X-RAY DIFFRACTION40P586 - 599
41X-RAY DIFFRACTION41I31 - 88
42X-RAY DIFFRACTION42I89 - 230
43X-RAY DIFFRACTION43I231 - 265
44X-RAY DIFFRACTION44I266 - 310
45X-RAY DIFFRACTION45K31 - 88
46X-RAY DIFFRACTION46K89 - 230
47X-RAY DIFFRACTION47K231 - 265
48X-RAY DIFFRACTION48K266 - 309
49X-RAY DIFFRACTION49M31 - 88
50X-RAY DIFFRACTION50M89 - 230
51X-RAY DIFFRACTION51M231 - 265
52X-RAY DIFFRACTION52M266 - 308
53X-RAY DIFFRACTION53O31 - 88
54X-RAY DIFFRACTION54O89 - 230
55X-RAY DIFFRACTION55O231 - 266
56X-RAY DIFFRACTION56O273 - 308

+
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