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- PDB-5cjx: Crystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 ... -

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基本情報

登録情報
データベース: PDB / ID: 5cjx
タイトルCrystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 HIV-1 Env trimer
要素
  • (8ANC195 G52K5 ...) x 2
  • BG505 Env gp120
  • BG505 Env gp41
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 Env trimer / IG fold / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane
類似検索 - 分子機能
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Envelope glycoprotein gp160
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.584 Å
データ登録者Scharf, L. / Bjorkman, P.J.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD P01 AI100148 米国
Bill & Melinda Gates Foundation1040753 米国
American Cancer SocietyPF-13-076-01-MPC 米国
引用ジャーナル: Cell / 年: 2015
タイトル: Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env.
著者: Louise Scharf / Haoqing Wang / Han Gao / Songye Chen / Alasdair W McDowall / Pamela J Bjorkman /
要旨: The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal ...The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal and electron microscopy (EM) structures of bNAb 8ANC195 complexed with monomeric gp120 and trimeric Env, respectively, spans the gp120 and gp41 Env subunits. To investigate 8ANC195's gp41 epitope at higher resolution, we solved a 3.58 Å crystal structure of 8ANC195 complexed with fully glycosylated Env trimer, revealing 8ANC195 insertion into a glycan shield gap to contact gp120 and gp41 glycans and protein residues. To determine whether 8ANC195 recognizes the CD4-bound open Env conformation that leads to co-receptor binding and fusion, one of several known conformations of virion-associated Env, we solved EM structures of an Env/CD4/CD4-induced antibody/8ANC195 complex. 8ANC195 binding partially closed the CD4-bound trimer, confirming structural plasticity of Env by revealing a previously unseen conformation. 8ANC195's ability to bind different Env conformations suggests advantages for potential therapeutic applications.
履歴
登録2015年7月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年9月23日Provider: repository / タイプ: Initial release
改定 1.12017年9月6日Group: Author supporting evidence / Derived calculations / カテゴリ: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.22019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
B: BG505 Env gp41
C: 8ANC195 G52K5 light chain
D: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
E: 8ANC195 G52K5 light chain
G: BG505 Env gp120
H: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
J: BG505 Env gp41
K: BG505 Env gp120
L: 8ANC195 G52K5 light chain
X: BG505 Env gp41
Y: BG505 Env gp120
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)377,12434
ポリマ－361,87212
非ポリマー15,25222
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area63960 Å2
ΔGint24 kcal/mol
Surface area124910 Å2
手法PISA
単位格子
Length a, b, c (Å)117.739, 195.224, 119.094
Angle α, β, γ (deg.)90.00, 101.60, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 2種, 6分子 BJXGKY

#2: タンパク質 BG505 Env gp41


分子量: 17146.482 Da / 分子数: 3 / Fragment: UNP residues 509-661 / Mutation: I559P, T605C / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 細胞株 (発現宿主): HEK293-6E / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6
#4: タンパク質 BG505 Env gp120


分子量: 53864.086 Da / 分子数: 3 / Fragment: UNP residues 32-505 / Mutation: T332N, A501C / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: env / 細胞株 (発現宿主): HEK293-6E / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6

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抗体 , 2種, 6分子 ADHCEL

#1: 抗体 8ANC195 G52K5 heavy chain, IG gamma-1 chain


分子量: 26153.283 Da / 分子数: 3 / 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): HEK293-6 / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 8ANC195 G52K5 light chain


分子量: 23460.047 Da / 分子数: 3 / 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): HEK293-6E / 発現宿主: Homo sapiens (ヒト)

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糖 , 7種, 22分子

#5: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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: 5 / 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
#7: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#8: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(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: 1072.964 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
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 748.682 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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 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: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#11: 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: 6 / 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

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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: 3.71 Å3/Da / 溶媒含有率: 66.8 %
結晶化温度: 298 K / 手法: 蒸気拡散法 / pH: 8 / 詳細: 0.1 M Tris, pH 8.0, 15% PEG3350, 2% v/v 1,4-dioxane

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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: APS / ビームライン: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年11月7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: 1.0332 Å / 相対比: 1
反射解像度: 3.584→29.735 Å / Num. all: 61166 / Num. obs: 61166 / % possible obs: 98.9 % / 冗長度: 3.4 % / Biso Wilson estimate: 130.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Net I/σ(I): 14.4 / Num. measured all: 201456
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.584-3.733.20.7531.71295941080.5540.49288.9
15.84-29.763.30.01666.821216450.9990.01185.1

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation7.19 Å29.74 Å
Translation7.19 Å29.74 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10pre_2100: ???)精密化
Aimless0.3.11データスケーリング
PHASER2.5.6位相決定
PDB_EXTRACT3.15データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: PDB entries 4TVP & 4P9M

4tvp

4p9m


解像度: 3.584→29.735 Å / SU ML: 0.54 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 30.52 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2862 2014 3.29 %
Rwork0.2386 --
obs0.2401 61155 99.03 %
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
精密化ステップサイクル: LAST / 解像度: 3.584→29.735 Å
タンパク質核酸リガンド溶媒全体
原子数21283 0 1016 0 22299
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00722893
X-RAY DIFFRACTIONf_angle_d0.85931495
X-RAY DIFFRACTIONf_dihedral_angle_d10.09413471
X-RAY DIFFRACTIONf_chiral_restr0.0493920
X-RAY DIFFRACTIONf_plane_restr0.0053880
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5835-3.6730.32151210.3413779X-RAY DIFFRACTION88
3.673-3.77210.36831510.32114199X-RAY DIFFRACTION100
3.7721-3.88290.39641440.31624246X-RAY DIFFRACTION100
3.8829-4.00790.3581440.29764250X-RAY DIFFRACTION100
4.0079-4.15080.30051490.27294254X-RAY DIFFRACTION100
4.1508-4.31650.28251410.24244251X-RAY DIFFRACTION100
4.3165-4.51230.28291470.2294228X-RAY DIFFRACTION100
4.5123-4.74930.25621450.22084288X-RAY DIFFRACTION100
4.7493-5.04550.24761470.20964244X-RAY DIFFRACTION100
5.0455-5.43290.26681420.21424278X-RAY DIFFRACTION100
5.4329-5.97570.27281470.23724268X-RAY DIFFRACTION100
5.9757-6.83120.30711470.2384243X-RAY DIFFRACTION100
6.8312-8.57230.29491460.22324286X-RAY DIFFRACTION100
8.5723-29.73620.26341430.22114327X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.86766.378-1.26177.0969-1.84680.83930.5062-2.54292.00060.5608-0.55590.7311-0.28130.31840.20271.5210.49640.26211.5873-0.24211.2609-5.833123.207777.4994
26.0184-0.5041-2.14024.50770.129.0274-0.2404-0.0079-0.0812-0.28010.46480.2033-0.9331-1.0449-0.26261.06550.4710.04561.11620.0110.7569-5.464521.992867.0548
31.21231.2568-1.95330.7517-3.0653.28190.4208-0.71960.4890.44870.58150.4008-0.3714-0.6098-1.00941.49490.38630.26951.61840.08060.87420.198618.817368.6916
44.0744-3.5044-1.3245.1692-1.19738.3606-0.22251.0977-0.1331-0.43960.0926-0.16590.27870.63140.10911.03440.27750.17181.542-0.01710.8186-2.92824.833198.8371
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85.18460.9736-3.38484.99314.65356.0614-0.14170.4911-0.0875-1.13250.2224-0.0397-0.1407-0.3502-0.18530.67-0.0193-0.07720.86560.13480.680915.667128.34210.9221
97.6301-6.31812.95871.9881-6.64364.867-1.7628-2.2869-1.11141.01151.9404-0.333-0.112-3.0067-0.31450.84460.00720.22421.14070.22731.01210.708426.864913.7485
106.66245.9844-1.59055.1328-1.19441.82532.15113.55930.6121.34632.26340.1336-1.2089-2.8937-2.46391.5389-0.2195-0.1171.1689-0.09360.97998.5919.272821.2966
115.8751-1.23811.83965.27331.55556.15140.2533-1.7378-1.11840.1043-0.1753-0.19241.01640.75490.08081.28220.42550.21431.67180.34480.784211.3093.381165.5662
126.1952-0.453-2.87181.307-1.85033.3608-1.065-1.6850.62481.97141.03-0.47110.90631.2057-0.01421.54850.6344-0.01911.6181-0.17350.827615.595411.092466.3975
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146.2230.42082.13831.4743-3.28976.0172-0.24430.6172-0.9748-0.751-0.15020.0691.4281.6320.44611.4750.45970.18861.2427-0.15810.90591.6716-6.113892.65
158.4331.4167-2.58634.7272-6.92968.0882-0.31390.3734-2.1492-2.0638-0.35930.3771.676-0.15530.76361.70690.0810.13181.3377-0.22641.1604-4.0333-13.85696.2358
163.9483-0.0232-2.20362.42471.69543.53070.1776-0.59330.50480.3653-0.3591-0.91290.23451.10440.30860.73470.1221-0.23091.67570.11911.495982.02119.621228.6719
173.0626-3.3687-4.11983.87644.71885.3227-0.4793-1.4003-0.02030.24360.91010.42460.72030.4809-0.17670.9550.2737-0.26161.5020.02881.304174.1812-0.219731.488
184.56540.2795-2.35253.0585-5.72632.4779-0.0213-3.0919-0.03680.329-3.1797-0.6807-0.6633.74011.48520.87740.7199-0.78553.0633-0.04621.498879.506512.329140.0708
191.895-0.0363-8.32273.68381.41366.6126-1.6787-0.7006-1.24480.2381-0.34852.7890.5728-0.37821.67020.94120.5404-0.0992.07630.20921.573387.0781-0.076528.8794
207.2761-2.0848-3.14987.8156-0.66546.5557-0.6204-2.8365-1.1586-0.3246-0.69950.0835-1.1691.37391.16860.89860.1409-0.1341.8419-0.10291.047869.35712.76126.524
218.3335-0.1978-2.8054-0.4162-0.4440.6944-0.8359-1.4034-0.0486-0.1860.0074-0.1090.13760.34470.87050.87790.0142-0.13652.29990.31181.77996.79067.159615.6513
223.71361.2983-0.78094.3728-4.80495.1935-0.7918-0.2422-0.6140.77221.88770.4602-0.655-2.0696-1.16831.08420.2170.05431.84980.48622.0965105.60659.402110.8403
238.48544.4029-5.16477.38751.61778.0892-0.92820.32-1.1534-2.47111.93540.7484-4.5317-2.7246-0.65841.33660.0414-0.03361.40140.64721.806113.934216.0472-2.0323
247.6276-0.1679-1.49316.09243.58592.20211.4117-0.8252-0.05040.0745-0.01070.9974-2.4005-3.3975-1.23311.31270.1128-0.22432.2818-0.00061.5333115.063411.121312.9967
256.73224.8623-5.67254.7917-3.12997.16930.0050.5867-1.0868-0.4649-0.3786-0.64410.19-0.12980.30850.7520.12280.13871.68840.14591.860771.25349.86137.2973
260.24740.41640.01683.60992.16461.5519-1.78810.88115.87433.05120.17161.3795-2.32562.3760.3748-1.7606-1.6492-0.57291.48570.99333.566373.041620.160814.8282
276.55590.0209-3.5913-0.62131.45745.71210.12841.41111.3479-0.314-0.0072-0.5454-0.34010.8172-0.10110.7509-0.03420.12631.78110.43171.644874.976913.0977.2202
289.8183-3.81111.02744.37891.67923.09480.86730.8639-0.11930.5269-0.5749-0.58050.6530.1216-0.21271.2879-0.3586-0.30051.89680.27492.104105.07510.4148-2.7831
292.12962.434-1.46543.2106-2.72242.5693-1.7986-0.5749-1.11040.64873.26222.3109-0.1804-1.6611-1.2251.3284-0.31560.06682.77180.58921.746195.83169.28931.5131
305.64711.06044.48836.28381.27993.72561.0101-0.3924-1.06520.2720.78370.49551.10060.6999-1.90921.240.0247-0.1152.3060.57361.4677105.4044-3.299-6.7256
313.09552.98451.65493.95882.1282.35880.6679-0.32050.38261.2036-0.1227-0.88730.19490.3757-0.56441.0796-0.1786-0.08141.0362-0.22051.586841.475950.430518.755
320.72122.52953.46651.86442.8512.452-0.6753-0.54170.8415-0.7045-0.04240.71510.5987-0.86570.68461.6784-0.4553-0.16251.3135-0.23382.051956.473872.162838.4437
336.46660.88813.03763.02353.88839.318-0.04780.6064-0.5531-0.47411.0682-2.3153-1.42921.9081-0.92950.9592-0.27090.09171.017-0.32611.848542.895647.101110.5333
340.90763.96321.92555.35213.06160.8735-0.06550.00740.2757-0.91050.0312-0.7777-0.770.4269-0.04511.0723-0.03680.32070.8933-0.00871.816742.963656.765.0713
350.96856.26943.0510.30281.18194.6463-0.76790.5061-0.031-0.35010.3657-0.1063-2.67321.88870.22921.30090.1889-0.29341.588-0.24541.706760.724565.410522.6988
367.40873.06154.78793.9878-0.76222.4272-1.48841.14032.8066-0.06170.2470.1647-0.26350.25171.46791.6208-0.6134-0.06491.52320.46182.32548.542271.3782-0.0157
371.9095-1.9879-0.42473.3845-4.39074.26690.7816-0.7111-0.37610.6081.35311.7411-1.9489-1.3919-2.1361.5479-0.74510.12151.56520.17842.612155.698872.30127.8702
383.96340.515-0.82055.2434-0.52064.1139-1.55211.4735-0.3336-0.8011.8398-2.27641.7939-0.5196-0.15832.1484-0.86510.0621.7808-0.44442.036953.543167.855127.8919
399.65170.89991.90631.16982.41447.0929-0.78980.69221.75981.0953-0.286-1.4941-2.36061.26220.96951.6534-0.56660.15560.90790.02451.874548.886469.64275.066
408.56354.29241.71949.37860.14432.30520.29540.37090.8060.8427-0.1236-0.5335-0.59390.5453-0.09911.1314-0.1267-0.07490.8121-0.01080.606931.752142.93519.8742
412.82660.18672.45550.5535-1.94522.85160.07581.28211.1302-1.1818-0.3236-0.5949-0.0610.63010.03291.7860.22940.46761.21320.31771.362614.534467.8952-18.0216
423.40710.38942.28982.6692-2.18372.4740.602-0.00280.8221-0.0666-0.9536-0.67460.51150.02830.25931.00380.10790.29810.9160.24250.973816.377458.2965-11.4212
433.10020.37810.09668.9164-5.04062.81640.54520.14550.1723-0.5869-1.0145-0.860.72050.36310.36911.38840.02970.20911.1370.40871.119523.060956.5246-15.2097
441.58490.437-0.02946.67991.87359.53740.64560.80830.3095-0.2588-0.6665-0.246-0.3205-0.2180.08090.98060.31760.41791.02260.36820.910716.135255.6116-11.4582
452.258-3.39592.84028.0756-2.33450.52630.99270.73450.3478-1.0075-1.87670.93530.3172.18010.55481.40620.170.18211.01640.47791.26299.872263.364-16.3344
468.1153-6.07310.02684.0066-2.13055.1340.28030.7438-1.3338-0.5224-0.47170.6732-0.0946-0.0349-0.06331.20790.14280.00610.6376-0.02170.6414-14.343781.6996-23.396
475.3536-0.9334-0.96436.3697-3.1756.6339-1.0541-0.7705-0.8202-0.39350.2054-0.35750.92430.83080.95641.250.05410.13620.9650.12230.9469-6.435277.9652-18.7219
489.6837-4.06861.77285.3476-5.62816.9106-0.914-0.59961.1229-0.3741-0.0456-0.9551-0.03670.66840.820.85920.1379-0.06240.87130.04880.9213-11.056786.2629-19.0579
497.51935.5298-1.98133.479-0.17819.4285-0.40460.08190.6242-1.13520.05970.615-2.01650.30190.29721.28630.1042-0.09511.1022-0.19840.73657.305324.006830.9958
505.31364.732-0.15223.20912.99377.3644-0.447-0.67411.2031-0.02310.53090.637-0.40840.10410.18540.82920.0452-0.06660.896-0.38451.001825.963429.417432.8464
514.1522-3.86143.41287.1611-0.94454.4439-0.3496-0.69790.11730.47610.55790.2643-0.4575-0.8066-0.19880.64060.10870.09520.69070.01190.61269.7629.639839.8649
521.98213.0229-2.41094.1715-3.98623.4751-1.1796-1.64790.5483-0.15931.6341-1.6964-1.10661.0363-0.28970.83530.0875-0.13791.1522-0.26110.753823.63387.983637.5366
533.2524-2.042-0.2515.64574.99845.2713-2.7742-0.8125-0.2470.05450.95560.114-0.66260.53131.87111.6676-0.13270.38030.973-0.20151.00730.8898-1.448622.1407
542.17551.3681-0.73115.4119-1.31611.0960.0648-0.3911.17540.91770.09940.0374-1.283-0.1887-0.09271.65750.1857-0.1020.9001-0.18661.265919.873547.146543.8946
552.82920.67890.45261.2517-0.19760.886-0.2078-0.47191.31960.204-0.1302-0.0196-1.10890.00970.31541.86950.1111-0.01810.9999-0.29541.449814.359356.182149.4697
563.4468-0.31510.09323.93091.5077-0.1673-0.87990.061-0.40370.65250.4466-0.43370.0755-0.18940.47832.02680.3446-0.09251.1673-0.41921.51899.38965.459556.6782
572.30050.6383-0.7601-0.5754-3.60920.38270.1511-0.5981.15390.424-0.19430.8899-1.36650.13190.01751.18560.1857-0.10841.0998-0.43181.182113.307846.285648.5312
589.2293-4.4467-4.38623.64521.46058.9925-0.320.7632-0.25160.42670.04440.88441.6072-1.0264-0.00531.13550.22050.1460.89330.22540.7059-6.564750.7773-4.6355
595.6998-1.46750.08617.2342-1.94623.96290.81440.6583-0.0467-0.5234-0.507-0.28010.64-0.0164-0.31641.07040.31240.14310.94260.350.90622.173345.6743-3.8336
602.9594-2.16034.10253.9096-4.17028.593-0.218-0.83241.63631.88791.3562-0.2721-2.7189-0.4714-0.69881.64450.09820.43280.73910.33191.35115.122556.09492.6123
618.9378-7.7114-4.05754.52794.16543.5121-0.1921-0.6538-0.12390.79040.45950.337-0.31490.0351-0.20751.22360.17370.16240.95170.3371.1098-2.090652.02630.6894
623.0528-4.82383.58269.8659-5.13362.0227-0.0639-0.0403-0.1245-1.06570.1230.56790.22740.4142-0.05021.12130.09920.01310.85430.08650.8478-10.373565.1203-16.314
637.7881-2.0945-3.09678.8648-1.67993.5685-0.22690.8058-1.4821-1.69750.51931.54592.1817-1.2563-0.61691.518-0.1981-0.08770.79260.08111.3556-21.402469.5277-22.6192
642.6661-4.3783-1.7874.04884.06571.0296-1.4168-0.36870.98940.8931-0.36831.2232-0.40280.1381.27661.5147-0.0356-0.38451.1596-0.49421.552840.590913.116935.0381
654.07711.1779-0.01472.14296.30684.2806-0.91920.35571.0851.389-0.0979-0.9020.49070.52041.07691.15530.0401-0.3381.0935-0.29071.370136.96526.977128.3278
663.67211.52722.83236.57523.47484.97310.27640.07770.26680.29370.2095-0.60860.50290.9788-0.53550.6532-0.015-0.08630.95450.0060.813745.68337.29217.5299
673.27341.93321.05923.5106-2.52623.84470.7862-0.2148-0.4555-2.6412-1.0467-1.17312.05671.1047-0.10131.35550.2134-0.21590.9547-0.23131.423626.28512.13493.6252
683.74050.2089-0.32745.2321-1.19525.35170.6595-0.93520.78961.667-0.2468-0.1025-1.0996-0.3459-0.35661.08340.0023-0.00051.2839-0.22861.005842.688818.693337.7925
69-0.5252-0.7239-0.05453.7817-0.26341.3928-0.0721-0.29990.34751.46190.0141-0.6914-0.56040.27050.02941.68310.0362-0.481.5538-0.59811.674754.289941.962653.6696
70-0.5887-1.9553-3.46325.02411.15611.5546-0.8327-1.21530.2621.09410.7064-0.02360.03441.2142-0.04871.5680.0149-0.62421.8419-0.44661.471264.698732.502561.2155
710.9265-1.1667-1.0751.9394-0.41151.3708-0.2779-1.04920.97331.13980.3363-1.0105-0.87090.9038-0.07611.4697-0.0853-0.47131.5437-0.48981.582559.13931.660852.638
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 213 )
6X-RAY DIFFRACTION6chain 'B' and (resid 519 through 571 )
7X-RAY DIFFRACTION7chain 'B' and (resid 572 through 600 )
8X-RAY DIFFRACTION8chain 'B' and (resid 601 through 638 )
9X-RAY DIFFRACTION9chain 'B' and (resid 639 through 650 )
10X-RAY DIFFRACTION10chain 'B' and (resid 651 through 664 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 38 )
12X-RAY DIFFRACTION12chain 'C' and (resid 39 through 75 )
13X-RAY DIFFRACTION13chain 'C' and (resid 76 through 101 )
14X-RAY DIFFRACTION14chain 'C' and (resid 102 through 172 )
15X-RAY DIFFRACTION15chain 'C' and (resid 173 through 213 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 51 )
17X-RAY DIFFRACTION17chain 'D' and (resid 52 through 66 )
18X-RAY DIFFRACTION18chain 'D' and (resid 67 through 77C)
19X-RAY DIFFRACTION19chain 'D' and (resid 77D through 87 )
20X-RAY DIFFRACTION20chain 'D' and (resid 88 through 100F)
21X-RAY DIFFRACTION21chain 'D' and (resid 100G through 143 )
22X-RAY DIFFRACTION22chain 'D' and (resid 144 through 177 )
23X-RAY DIFFRACTION23chain 'D' and (resid 178 through 194 )
24X-RAY DIFFRACTION24chain 'D' and (resid 195 through 213 )
25X-RAY DIFFRACTION25chain 'E' and (resid 1 through 38 )
26X-RAY DIFFRACTION26chain 'E' and (resid 39 through 61 )
27X-RAY DIFFRACTION27chain 'E' and (resid 62 through 113 )
28X-RAY DIFFRACTION28chain 'E' and (resid 114 through 155 )
29X-RAY DIFFRACTION29chain 'E' and (resid 156 through 174 )
30X-RAY DIFFRACTION30chain 'E' and (resid 175 through 213 )
31X-RAY DIFFRACTION31chain 'G' and (resid 33 through 162 )
32X-RAY DIFFRACTION32chain 'G' and (resid 163 through 208 )
33X-RAY DIFFRACTION33chain 'G' and (resid 209 through 235 )
34X-RAY DIFFRACTION34chain 'G' and (resid 236 through 283 )
35X-RAY DIFFRACTION35chain 'G' and (resid 284 through 334 )
36X-RAY DIFFRACTION36chain 'G' and (resid 335 through 375 )
37X-RAY DIFFRACTION37chain 'G' and (resid 376 through 417 )
38X-RAY DIFFRACTION38chain 'G' and (resid 418 through 442 )
39X-RAY DIFFRACTION39chain 'G' and (resid 443 through 470 )
40X-RAY DIFFRACTION40chain 'G' and (resid 471 through 505 )
41X-RAY DIFFRACTION41chain 'H' and (resid 1 through 17 )
42X-RAY DIFFRACTION42chain 'H' and (resid 18 through 52 )
43X-RAY DIFFRACTION43chain 'H' and (resid 54 through 77C)
44X-RAY DIFFRACTION44chain 'H' and (resid 77D through 100F)
45X-RAY DIFFRACTION45chain 'H' and (resid 100G through 119 )
46X-RAY DIFFRACTION46chain 'H' and (resid 120 through 145 )
47X-RAY DIFFRACTION47chain 'H' and (resid 146 through 175 )
48X-RAY DIFFRACTION48chain 'H' and (resid 176 through 214 )
49X-RAY DIFFRACTION49chain 'J' and (resid 520 through 544 )
50X-RAY DIFFRACTION50chain 'J' and (resid 545 through 600 )
51X-RAY DIFFRACTION51chain 'J' and (resid 601 through 638 )
52X-RAY DIFFRACTION52chain 'J' and (resid 639 through 651 )
53X-RAY DIFFRACTION53chain 'J' and (resid 652 through 664 )
54X-RAY DIFFRACTION54chain 'K' and (resid 33 through 162 )
55X-RAY DIFFRACTION55chain 'K' and (resid 163 through 298 )
56X-RAY DIFFRACTION56chain 'K' and (resid 299 through 428 )
57X-RAY DIFFRACTION57chain 'K' and (resid 429 through 505 )
58X-RAY DIFFRACTION58chain 'L' and (resid 1 through 18 )
59X-RAY DIFFRACTION59chain 'L' and (resid 19 through 38 )
60X-RAY DIFFRACTION60chain 'L' and (resid 39 through 61 )
61X-RAY DIFFRACTION61chain 'L' and (resid 62 through 90 )
62X-RAY DIFFRACTION62chain 'L' and (resid 91 through 128 )
63X-RAY DIFFRACTION63chain 'L' and (resid 129 through 213 )
64X-RAY DIFFRACTION64chain 'X' and (resid 521 through 571 )
65X-RAY DIFFRACTION65chain 'X' and (resid 572 through 595 )
66X-RAY DIFFRACTION66chain 'X' and (resid 596 through 648 )
67X-RAY DIFFRACTION67chain 'X' and (resid 649 through 664 )
68X-RAY DIFFRACTION68chain 'Y' and (resid 33 through 86 )
69X-RAY DIFFRACTION69chain 'Y' and (resid 87 through 258 )
70X-RAY DIFFRACTION70chain 'Y' and (resid 259 through 380 )
71X-RAY DIFFRACTION71chain 'Y' and (resid 381 through 505 )

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万見について

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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://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

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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

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