[日本語] English
万見
- PDB-6nz7: Crystal structure of broadly neutralizing Influenza A antibody 42... -

+
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: 6nz7
タイトルCrystal structure of broadly neutralizing Influenza A antibody 429 B01 in complex with Hemagglutinin Hong Kong 1968
要素
  • (Hemagglutinin ...) x 2
  • 429 B01 FAB heavy chain
  • 429 B01 FAB light chain
キーワードIMMUNE SYSTEM / Antibody / Influenza / neutralization
機能・相同性
機能・相同性情報


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region ...viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / metal ion binding / membrane / plasma membrane
類似検索 - 分子機能
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / : / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein ...Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / : / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Ig-like domain-containing protein / Ig-like domain-containing protein / Hemagglutinin
類似検索 - 構成要素
生物種Influenza A virus (A型インフルエンザウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.95 Å
データ登録者Zhou, T. / Kwong, P.D.
引用ジャーナル: Sci Immunol / 年: 2019
タイトル: Prolonged evolution of the memory B cell response induced by a replicating adenovirus-influenza H5 vaccine.
著者: Matsuda, K. / Huang, J. / Zhou, T. / Sheng, Z. / Kang, B.H. / Ishida, E. / Griesman, T. / Stuccio, S. / Bolkhovitinov, L. / Wohlbold, T.J. / Chromikova, V. / Cagigi, A. / Leung, K. / Andrews, ...著者: Matsuda, K. / Huang, J. / Zhou, T. / Sheng, Z. / Kang, B.H. / Ishida, E. / Griesman, T. / Stuccio, S. / Bolkhovitinov, L. / Wohlbold, T.J. / Chromikova, V. / Cagigi, A. / Leung, K. / Andrews, S. / Cheung, C.S.F. / Pullano, A.A. / Plyler, J. / Soto, C. / Zhang, B. / Yang, Y. / Joyce, M.G. / Tsybovsky, Y. / Wheatley, A. / Narpala, S.R. / Guo, Y. / Darko, S. / Bailer, R.T. / Poole, A. / Liang, C.J. / Smith, J. / Alexander, J. / Gurwith, M. / Migueles, S.A. / Koup, R.A. / Golding, H. / Khurana, S. / McDermott, A.B. / Shapiro, L. / Krammer, F. / Kwong, P.D. / Connors, M.
履歴
登録2019年2月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年5月8日Provider: repository / タイプ: Initial release
改定 1.12020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.22024年10月16日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: 429 B01 FAB heavy chain
L: 429 B01 FAB light chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: 429 B01 FAB heavy chain
I: 429 B01 FAB light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)207,65119
ポリマ－205,2178
非ポリマー2,43311
水34219
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: 429 B01 FAB heavy chain
L: 429 B01 FAB light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)103,93610
ポリマ－102,6094
非ポリマー1,3276
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-39 kcal/mol
Surface area42440 Å2
手法PISA
2
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: 429 B01 FAB heavy chain
I: 429 B01 FAB light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)103,7159
ポリマ－102,6094
非ポリマー1,1065
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-49 kcal/mol
Surface area42300 Å2
手法PISA
単位格子
Length a, b, c (Å)91.769, 123.905, 119.338
Angle α, β, γ (deg.)90.000, 112.000, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain G and (resseq 1:126 or resseq 128 or resseq...
21(chain H and (resseq 1:126 or resseq 128 or resseq...
12(chain L and (resseq 2:52 or resseq 54:108 or (resid...
22(chain I and (resseq 2:52 or resseq 54:108 or (resid...
13(chain B and (resseq 4:18 or resseq 20:61 or (resid...
23(chain F and (resseq 4:18 or resseq 20:61 or (resid...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain G and (resseq 1:126 or resseq 128 or resseq...G1 - 126
121(chain G and (resseq 1:126 or resseq 128 or resseq...G128
131(chain G and (resseq 1:126 or resseq 128 or resseq...G130 - 137
141(chain G and (resseq 1:126 or resseq 128 or resseq...G147 - 200
151(chain G and (resseq 1:126 or resseq 128 or resseq...G202 - 217
161(chain G and (resseq 1:126 or resseq 128 or resseq...G219 - 225
211(chain H and (resseq 1:126 or resseq 128 or resseq...H1 - 126
221(chain H and (resseq 1:126 or resseq 128 or resseq...H128
231(chain H and (resseq 1:126 or resseq 128 or resseq...H130 - 137
241(chain H and (resseq 1:126 or resseq 128 or resseq...H147 - 200
251(chain H and (resseq 1:126 or resseq 128 or resseq...H202 - 217
261(chain H and (resseq 1:126 or resseq 128 or resseq...H219 - 225
112(chain L and (resseq 2:52 or resseq 54:108 or (resid...L2 - 52
122(chain L and (resseq 2:52 or resseq 54:108 or (resid...L54 - 108
132(chain L and (resseq 2:52 or resseq 54:108 or (resid...L0
142(chain L and (resseq 2:52 or resseq 54:108 or (resid...L1 - 214
152(chain L and (resseq 2:52 or resseq 54:108 or (resid...L1 - 214
162(chain L and (resseq 2:52 or resseq 54:108 or (resid...L1 - 214
172(chain L and (resseq 2:52 or resseq 54:108 or (resid...L1 - 214
182(chain L and (resseq 2:52 or resseq 54:108 or (resid...L1 - 214
192(chain L and (resseq 2:52 or resseq 54:108 or (resid...L1 - 214
212(chain I and (resseq 2:52 or resseq 54:108 or (resid...I2 - 52
222(chain I and (resseq 2:52 or resseq 54:108 or (resid...I54 - 108
232(chain I and (resseq 2:52 or resseq 54:108 or (resid...I109
242(chain I and (resseq 2:52 or resseq 54:108 or (resid...I1 - 214
252(chain I and (resseq 2:52 or resseq 54:108 or (resid...I1 - 214
262(chain I and (resseq 2:52 or resseq 54:108 or (resid...I1 - 214
272(chain I and (resseq 2:52 or resseq 54:108 or (resid...I1 - 214
113(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 18
123(chain B and (resseq 4:18 or resseq 20:61 or (resid...B20 - 61
133(chain B and (resseq 4:18 or resseq 20:61 or (resid...B62
143(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 654
153(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 654
163(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 654
173(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 654
183(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 654
193(chain B and (resseq 4:18 or resseq 20:61 or (resid...B4 - 654
213(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 18
223(chain F and (resseq 4:18 or resseq 20:61 or (resid...F20 - 61
233(chain F and (resseq 4:18 or resseq 20:61 or (resid...F62
243(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 654
253(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 654
263(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 654
273(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 654
283(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 654
293(chain F and (resseq 4:18 or resseq 20:61 or (resid...F4 - 654

NCSアンサンブル:
ID
1
2
3

-
要素

-
Hemagglutinin ... , 2種, 4分子 AEBF

#1: タンパク質 Hemagglutinin HA1 chain


分子量: 35154.539 Da / 分子数: 2 / 断片: residues 24-342 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) (A型インフルエンザウイルス)
株: A/Hong Kong/1/1968 H3N2 / 遺伝子: HA / 細胞株 (発現宿主): 293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q91MA7
#2: タンパク質 Hemagglutinin HA2 chain


分子量: 19980.070 Da / 分子数: 2 / 断片: residues 349-521 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) (A型インフルエンザウイルス)
株: A/Hong Kong/1/1968 H3N2 / 遺伝子: HA / 細胞株 (発現宿主): 293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q91MA7

-
抗体 , 2種, 4分子 HGLI

#3: 抗体 429 B01 FAB heavy chain


分子量: 24123.068 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): 293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A8K008
#4: 抗体 429 B01 FAB light chain


分子量: 23350.951 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pVRC8400 / 細胞株 (発現宿主): 293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8TCD0

-
糖 / 非ポリマー , 2種, 30分子

#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: 11 / 由来タイプ: 組換発現 / 式: C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
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
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 19 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
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: 2.83 Å3/Da / 溶媒含有率: 56.47 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 10 % PEG8000 (w/v), 100 mM Tris/Cl, pH 8.5 and 7.5 % 1,6-hexanediol (w/v)

-
データ収集

回折平均測定温度: 100 K / Ambient temp details: liquid nitrogen stream / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 325 mm CCD / 検出器: CCD / 日付: 2017年3月23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: 1 Å / 相対比: 1
反射解像度: 2.95→50 Å / Num. obs: 49672 / % possible obs: 94.7 % / 冗長度: 3.1 % / Biso Wilson estimate: 89.08 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.069 / Rrim(I) all: 0.126 / Χ2: 2.192 / Net I/σ(I): 8.5
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-31.70.50915430.70.4170.6611.03559.3
3-3.061.80.47918790.7820.3770.6121.01271.6
3.06-3.1120.47421590.8230.3590.5970.93183.1
3.11-3.182.30.55624420.7580.4160.6980.91993.2
3.18-3.252.50.54725530.740.3970.6790.95197.4
3.25-3.322.90.48625630.8540.340.5950.93898.9
3.32-3.413.10.44426200.8890.2970.5361.05699.7
3.41-3.53.30.39225860.9070.2560.471.37999.8
3.5-3.63.50.32426270.9360.2020.3821.26299.9
3.6-3.723.50.30925950.9440.1930.3651.86899.8
3.72-3.853.60.24526290.9670.1520.2891.699.8
3.85-43.60.21226120.9660.1330.2512.19299.8
4-4.193.60.14726120.9840.0920.1732.17499.8
4.19-4.413.50.11626140.9870.0740.1372.57299.8
4.41-4.683.50.09926120.9890.0640.1183.09499.5
4.68-5.043.40.09226100.9870.060.113.25199.6
5.04-5.553.50.08326150.990.0540.0993.19799.4
5.55-6.353.50.07826390.990.050.0933.22899.5
6.35-83.40.06726200.990.0440.083.42399.4
8-5030.05225420.9930.0360.0633.82493.8

-
解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155)精密化
HKL-2000データ削減
SCALEPACK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 / 解像度: 2.95→42.225 Å / SU ML: 0.45 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 33.59
Rfactor反射数%反射
Rfree0.2674 2503 5.05 %
Rwork0.2236 --
obs0.2258 49589 93.51 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 293.64 Å2 / Biso mean: 124.2972 Å2 / Biso min: 52.74 Å2
精密化ステップサイクル: final / 解像度: 2.95→42.225 Å
タンパク質核酸リガンド溶媒全体
原子数14125 0 154 19 14298
Biso mean--106.41 90.73 -
残基数----1829
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00514608
X-RAY DIFFRACTIONf_angle_d0.819876
X-RAY DIFFRACTIONf_chiral_restr0.0492261
X-RAY DIFFRACTIONf_plane_restr0.0042563
X-RAY DIFFRACTIONf_dihedral_angle_d13.7078733
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11G2078X-RAY DIFFRACTION8.741TORSIONAL
12H2078X-RAY DIFFRACTION8.741TORSIONAL
21L1997X-RAY DIFFRACTION8.741TORSIONAL
22I1997X-RAY DIFFRACTION8.741TORSIONAL
31B1421X-RAY DIFFRACTION8.741TORSIONAL
32F1421X-RAY DIFFRACTION8.741TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9347-2.99110.4116600.37191325138547
2.9911-3.05220.41121160.35731980209671
3.0522-3.11850.37991330.34612282241583
3.1185-3.1910.35791390.34782628276794
3.191-3.27080.37051300.3312762289298
3.2708-3.35920.33181330.30832766289999
3.3592-3.4580.31971400.29542773291399
3.458-3.56960.35561540.298727792933100
3.5696-3.69710.2511320.287727712903100
3.6971-3.8450.31271320.27628372969100
3.845-4.01990.2921790.261327432922100
4.0199-4.23160.27831550.223727632918100
4.2316-4.49650.30891370.205927902927100
4.4965-4.84320.24231570.19192795295299
4.8432-5.32970.26721840.188727502934100
5.3297-6.0990.22691560.20562791294799
6.099-7.67650.26761270.2042846297399
7.6765-42.22910.18321390.15362705284494
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)
11.262-1.23661.88290.9729-1.14582.8262-0.07150.2831-0.06330.18270.12680.3764-0.5018-0.3007-0.00020.8289-0.0220.07550.9484-0.0770.803811.4442-40.806313.0931
25.3453-1.085-0.61022.65090.74754.53930.17280.2408-0.1506-0.4045-0.29280.0709-0.6485-0.1793-00.8453-0.00030.01680.55890.01380.901810.5724-10.4364-35.0111
3-0.36070.095-0.8191.2787-1.15922.6958-0.0391-0.1930.11980.2576-0.0482-0.1739-0.2293-0.2074-00.7409-0.0706-0.05681.04740.14220.883213.0281-26.6209-6.3244
40.0511-0.1359-0.11760.64650.07020.5824-0.0814-0.1168-0.72060.26650.5263-0.3382-0.2985-0.27130.27380.42291.27410.6621.7893-0.31951.274510.2363-57.386736.0271
50.01340.0106-0.00120.03710.01330.02360.89540.6773-0.59590.8642-0.0830.9593-0.8255-0.27560.00131.2381-0.41950.17741.4441-0.04791.14449.0197-58.370226.0673
62.9291-0.58790.61910.7365-1.02211.4549-0.1937-0.8673-1.1735-0.90470.71721.5222-2.3983-1.26690.13491.12490.17450.07120.5903-0.04770.723716.3754-48.352826.9603
70.2532-0.3693-0.04090.5142-0.10440.17120.1463-1.26110.0681.0213-0.8206-0.1539-0.30810.33960.00221.2266-0.1067-0.01971.0585-0.05460.772219.0058-56.315839.6047
83.4979-1.06120.46082.0589-0.97330.90060.36521.32310.1241-0.7703-0.7401-0.06240.71111.6959-0.00930.92-0.00430.03361.0914-0.12690.763419.8119-45.18961.9303
91.942-0.12820.99070.03940.00310.83210.01740.17790.0521-0.7539-0.1376-0.14481.1893-0.7531-0.00010.98090.0608-0.03361.0276-0.11260.603515.2971-54.15759.3536
102.1606-0.21521.24030.1786-0.35771.0392-0.998-1.6613-0.34750.40450.6621-0.3644-0.9079-0.6808-0.01571.1144-0.1283-0.13150.7613-0.03420.870418.5347-65.452337.8648
110.25740.20960.38520.1680.30640.6078-0.6536-0.6681.77581.5423-0.1086-1.8032-1.38072.3058-0.07761.2444-0.1495-0.22150.8623-0.03690.921527.3804-57.609637.8437
121.2978-0.8835-0.35360.84990.03940.2681-0.0013-0.0644-1.51131.3915-0.0384-0.81050.44971.3132-0.00221.123-0.0862-0.1671.120.02071.031528.2577-70.823239.1537
131.81050.67350.34355.35770.54753.94350.107-0.6614-0.06441.4718-0.2203-0.6585-0.1073-0.0395-0.00011.3505-0.1562-0.20250.6863-0.02670.862632.729-29.511333.9676
140.62660.4581-0.13121.7166-0.81460.976-0.6687-0.6329-0.51121.73670.1498-1.14640.61850.1250.00051.7303-0.0569-0.44730.7254-0.00771.172834.4981-37.876637.2041
151.31282.0130.21742.9447-0.84761.53820.4467-0.1728-0.13121.2236-0.3649-0.6236-0.0230.30930.00081.3178-0.0121-0.22070.7131-0.05911.046332.4389-32.248431.0834
161.4591-0.506-1.41622.10580.91351.5244-0.3247-0.8384-1.3470.73320.9174-1.1367-0.17410.50720.26942.0835-0.4481-0.59190.29460.13881.457844.6753-18.050139.0391
170.36940.40630.26710.96110.56670.56270.1899-0.22690.42070.9189-0.5004-0.7425-0.5078-1.14990.00011.6736-0.0515-0.34221.1275-0.11612.105245.4226-1.706129.5684
181.19950.6588-0.34240.38-0.77822.0432-0.3906-0.36870.2610.62010.1435-0.7997-0.4984-2.6007-0.01161.78850.0621-0.14661.1464-0.08391.840142.2315-2.329529.5873
193.39741.4914-0.11983.87051.0285.16840.09570.689-0.2046-0.90660.0514-1.2-0.85440.11120.00020.9507-0.19820.31290.8769-0.07511.054436.5832-30.702610.6173
200.7182-0.1724-0.39450.1530.20380.17750.5160.131-0.11851.76-0.14-1.5358-0.55091.04230.00060.9321-0.0281-0.02390.7649-0.14221.175738.8684-35.583619.1295
210.20020.32550.46634.92211.94091.5307-0.32750.101-0.6933-1.6694-0.5492-1.3097-1.5743-0.5584-0.49031.4988-0.57980.61631.04680.01861.851747.1809-12.96766.0688
220.8770.2810.29240.24480.34470.4633-0.51090.05630.79710.9272-0.2368-1.0467-0.903-0.0647-0.55392.18450.0119-0.80990.0272-0.74422.570454.51844.889729.7459
238.47084.19455.74987.10194.4474.5243-1.62122.5268-0.006-0.78641.1216-1.9792-0.84162.0495-0.23531.671-0.26570.69430.4249-0.09382.921157.207-4.512517.933
240.1364-0.2367-0.02270.37660.03380.7363-0.07431.16671.5996-0.24311.0607-1.91320.70770.96790.02431.3178-0.01520.23011.0180.10083.203564.416-4.677524.1716
250.1590.07440.03440.05980.06670.06060.5109-1.1925-0.3864-1.1366-0.23410.1598-1.2054-0.5613-0.00071.8427-0.23740.7621.1838-0.0551.599643.9759-10.405312.6152
260.67650.907-0.19181.0342-0.29695.38030.5380.3345-1.67641.93980.1043-0.7638-0.20062.2875-0.09181.5057-0.1376-0.22430.8877-0.18062.733563.28332.133426.9364
273.45231.1954-0.10960.38650.0457-0.0472-1.85411.53670.57130.0329-0.0804-1.3342-0.32910.3717-0.70811.9207-0.39640.10650.9547-0.59732.809660.71315.309214.9705
282.13481.36941.08224.05371.32451.56970.17370.7188-1.00520.2177-0.168-0.08880.3870.228400.8406-0.10970.31451.5649-0.32321.2951-11.8499-24.05846.0219
290.1791-0.45750.43321.658-1.26010.977-0.23952.2074-0.834-0.42790.3611-0.0535-0.2360.7190.00181.63010.2953-0.32622.4163-1.0351.9119-22.6012-29.7383-14.6045
302.9502-0.22220.50291.26140.69870.3508-0.19570.8484-0.85210.3675-0.04850.3539-0.21350.3698-0.00151.0417-0.16070.25971.3835-0.11110.9896-10.2444-14.493811.4076
310.0457-0.0811-0.02380.07040.02130.0370.5772-0.4934-0.2512-1.2569-0.3352-1.79080.90490.58760.00141.8277-0.2286-0.54491.7960.19921.461621.512522.95137.5806
320.4454-0.29940.13250.28580.0066-0.0079-0.2599-0.48450.28240.11760.13370.316-0.53651.58830.00021.7348-0.3974-0.47391.35940.21941.054416.632816.767646.2885
33-0.02340.08020.00081.6763-1.58871.24390.0489-0.72480.14320.0321-0.88180.0161.1396-2.4962-0.01241.1371-0.2467-0.03231.71910.08380.8677-9.16938.287723.0362
340.7438-1.03341.17262.6669-1.99321.4163-0.3027-0.00190.0960.8201-0.1096-0.20580.01940.7119-0.24061.392-0.3078-0.29321.50.19030.84660.291216.281524.5627
352.8425-0.06880.66150.17960.12461.3345-0.8274-0.76111.4437-0.1564-0.1589-0.2588-1.37180.3117-0.11582.4956-0.4437-0.90121.2240.32681.438614.872329.218952.47
361.8334-0.7322-0.32180.40150.08280.0870.7087-0.44610.8726-0.1676-0.0965-1.11930.92631.52560.02972.7229-0.0654-0.74031.5535-0.19411.445112.371936.779459.9268
373.7293-0.07431.01483.631-0.54653.2289-0.03940.2303-0.2210.0252-0.1511-0.6701-0.07760.4529-0.00020.9582-0.1603-0.12810.86410.11430.87926.9526-5.769856.4283
381.01860.4310.5251.9976-0.54721.63730.36040.13010.8848-0.4007-0.9943-0.3007-0.30680.37310.00111.0797-0.112-0.22670.97650.18331.0168.48591.65760.021
390.55730.5819-0.1130.5377-0.96881.298-0.13240.2690.52540.16050.109-0.1529-0.2345-0.4646-0.00031.0245-0.1395-0.13670.96990.16950.94694.6722-5.759760.8239
400.93390.40480.37420.37410.13170.184-0.29680.665-0.55060.0745-0.3468-0.5313-0.08930.04770.0010.9517-0.0009-0.01921.0120.1370.99594.0317-3.447449.0979
410.3655-0.0158-0.20670.3863-0.40460.46570.2583-0.6299-0.98181.3746-0.1363-0.7580.9439-0.33660.00030.97930.0806-0.04470.7970.11051.4009-0.8791-29.354169.9302
420.6903-0.4587-0.13830.65560.50880.2985-0.47631.2183-0.399-0.17730.50090.34790.36851.16350.00151.1349-0.04080.05680.9261-0.16191.5073-4.7058-33.425359.5674
430.41120.47910.31931.4049-0.06910.284-0.110.4993-0.88290.96290.187-0.13432.36080.501-0.00031.2103-0.0172-0.25671.018-0.16921.4119-8.3441-28.436760.0753
440.47490.6914-0.54560.5221-0.53231.0287-0.32580.7252-0.4997-0.01420.5347-1.08220.91981.42980.00281.34190.2811-0.10561.367-0.43111.782-2.2105-37.986557.189
454.56672.05730.77954.3388-2.66283.1887-0.15560.70020.1998-0.57180.18310.5835-0.1098-0.57760.00021.0655-0.0949-0.2481.29540.15070.8241-11.2815-3.656543.6503
460.41810.21850.49090.4044-0.32610.80970.95461.99390.21570.9166-0.75540.99230.858-0.0243-0.01221.0069-0.3296-0.17381.95870.01221.1308-22.2252-21.292145.9952
470.2236-0.1493-0.09830.51310.16050.0679-0.32311.3637-1.90470.84330.1472-1.28461.78871.0220.0011.7196-0.0661-0.10431.1765-0.15771.8238-11.0787-41.639565.6718
481.18420.05770.79291.3321-0.50650.53950.11990.028-0.6033-0.1463-0.32110.75730.1245-1.7946-0.00131.11170.028-0.1791.2634-0.02531.58-22.966-33.326562.3509
490.1554-0.4160.23141.4289-0.70680.44210.20411.1102-0.6710.0513-0.77320.14881.16350.4451-0.0091.1572-0.1076-0.17911.1939-0.16781.3672-17.3203-26.058455.4158
502.29350.8848-1.70071.18320.14591.72850.3516-0.1076-1.17070.6301-0.01630.84091.1702-0.457-0.00011.5568-0.1624-0.16760.88420.03381.6522-22.1149-40.296366.048
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 57 )A8 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 249 )A58 - 249
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 326 )A250 - 326
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 8 )B4 - 8
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 13 )B9 - 13
6X-RAY DIFFRACTION6chain 'B' and (resid 14 through 22 )B14 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 30 )B23 - 30
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 81 )B31 - 81
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 132 )B82 - 132
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 145 )B133 - 145
11X-RAY DIFFRACTION11chain 'B' and (resid 146 through 153 )B146 - 153
12X-RAY DIFFRACTION12chain 'B' and (resid 154 through 170 )B154 - 170
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 57 )H1 - 57
14X-RAY DIFFRACTION14chain 'H' and (resid 58 through 75 )H58 - 75
15X-RAY DIFFRACTION15chain 'H' and (resid 76 through 115 )H76 - 115
16X-RAY DIFFRACTION16chain 'H' and (resid 116 through 131 )H116 - 131
17X-RAY DIFFRACTION17chain 'H' and (resid 132 through 169 )H132 - 169
18X-RAY DIFFRACTION18chain 'H' and (resid 170 through 227 )H170 - 227
19X-RAY DIFFRACTION19chain 'L' and (resid 1 through 84 )L1 - 84
20X-RAY DIFFRACTION20chain 'L' and (resid 85 through 102 )L85 - 102
21X-RAY DIFFRACTION21chain 'L' and (resid 103 through 113 )L103 - 113
22X-RAY DIFFRACTION22chain 'L' and (resid 114 through 128 )L114 - 128
23X-RAY DIFFRACTION23chain 'L' and (resid 129 through 150 )L129 - 150
24X-RAY DIFFRACTION24chain 'L' and (resid 151 through 163 )L151 - 163
25X-RAY DIFFRACTION25chain 'L' and (resid 164 through 174 )L164 - 174
26X-RAY DIFFRACTION26chain 'L' and (resid 175 through 197 )L175 - 197
27X-RAY DIFFRACTION27chain 'L' and (resid 198 through 214 )L198 - 214
28X-RAY DIFFRACTION28chain 'E' and (resid 8 through 195 )E8 - 195
29X-RAY DIFFRACTION29chain 'E' and (resid 196 through 228 )E196 - 228
30X-RAY DIFFRACTION30chain 'E' and (resid 229 through 326 )E229 - 326
31X-RAY DIFFRACTION31chain 'F' and (resid 4 through 13 )F4 - 13
32X-RAY DIFFRACTION32chain 'F' and (resid 14 through 37 )F14 - 37
33X-RAY DIFFRACTION33chain 'F' and (resid 38 through 81 )F38 - 81
34X-RAY DIFFRACTION34chain 'F' and (resid 82 through 126 )F82 - 126
35X-RAY DIFFRACTION35chain 'F' and (resid 127 through 158 )F127 - 158
36X-RAY DIFFRACTION36chain 'F' and (resid 159 through 165 )F159 - 165
37X-RAY DIFFRACTION37chain 'G' and (resid 1 through 58 )G1 - 58
38X-RAY DIFFRACTION38chain 'G' and (resid 59 through 76 )G59 - 76
39X-RAY DIFFRACTION39chain 'G' and (resid 77 through 100 )G77 - 100
40X-RAY DIFFRACTION40chain 'G' and (resid 101 through 123 )G101 - 123
41X-RAY DIFFRACTION41chain 'G' and (resid 124 through 136 )G124 - 136
42X-RAY DIFFRACTION42chain 'G' and (resid 137 through 169 )G137 - 169
43X-RAY DIFFRACTION43chain 'G' and (resid 170 through 187 )G170 - 187
44X-RAY DIFFRACTION44chain 'G' and (resid 188 through 227 )G188 - 227
45X-RAY DIFFRACTION45chain 'I' and (resid 1 through 101 )I1 - 101
46X-RAY DIFFRACTION46chain 'I' and (resid 102 through 113 )I102 - 113
47X-RAY DIFFRACTION47chain 'I' and (resid 114 through 128 )I114 - 128
48X-RAY DIFFRACTION48chain 'I' and (resid 129 through 155 )I129 - 155
49X-RAY DIFFRACTION49chain 'I' and (resid 156 through 174 )I156 - 174
50X-RAY DIFFRACTION50chain 'I' and (resid 175 through 214 )I175 - 214

+
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

+
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