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- PDB-6bf4: Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Co... -

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基本情報

登録情報
データベース: PDB / ID: 6bf4
タイトルCrystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120
要素
  • (VRC-PG05 Fab ...) x 2
  • HIV-1 clade AE gp120 core
キーワードviral protein/immune system / Antibody / HIV-1 / Silent face / glycan / gp120 / viral protein-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


positive regulation of establishment of T cell polarity / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / apoptotic process ...positive regulation of establishment of T cell polarity / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / apoptotic process / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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
ACETATE ION / Envelope glycoprotein gp160
類似検索 - 構成要素
生物種Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.382 Å
データ登録者Zhou, T. / Kwong, P.D.
引用ジャーナル: Immunity / 年: 2018
タイトル: A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.
著者: Zhou, T. / Zheng, A. / Baxa, U. / Chuang, G.Y. / Georgiev, I.S. / Kong, R. / O'Dell, S. / Shahzad-Ul-Hussan, S. / Shen, C.H. / Tsybovsky, Y. / Bailer, R.T. / Gift, S.K. / Louder, M.K. / ...著者: Zhou, T. / Zheng, A. / Baxa, U. / Chuang, G.Y. / Georgiev, I.S. / Kong, R. / O'Dell, S. / Shahzad-Ul-Hussan, S. / Shen, C.H. / Tsybovsky, Y. / Bailer, R.T. / Gift, S.K. / Louder, M.K. / McKee, K. / Rawi, R. / Stevenson, C.H. / Stewart-Jones, G.B.E. / Taft, J.D. / Waltari, E. / Yang, Y. / Zhang, B. / Shivatare, S.S. / Shivatare, V.S. / Lee, C.D. / Wu, C.Y. / Mullikin, J.C. / Bewley, C.A. / Burton, D.R. / Polonis, V.R. / Shapiro, L. / Wong, C.H. / Mascola, J.R. / Kwong, P.D. / Wu, X.
履歴
登録2017年10月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年3月7日Provider: repository / タイプ: Initial release
改定 1.12018年4月18日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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 / 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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _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_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10月4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11月20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

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集合体

登録構造単位
A: HIV-1 clade AE gp120 core
B: VRC-PG05 Fab heavy chain
C: VRC-PG05 Fab light chain
G: HIV-1 clade AE gp120 core
H: VRC-PG05 Fab heavy chain
L: VRC-PG05 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,01236
ポリマ－174,3786
非ポリマー13,63330
水3,171176
1
A: HIV-1 clade AE gp120 core
B: VRC-PG05 Fab heavy chain
C: VRC-PG05 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,76118
ポリマ－87,1893
非ポリマー6,57215
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
G: HIV-1 clade AE gp120 core
H: VRC-PG05 Fab heavy chain
L: VRC-PG05 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,25118
ポリマ－87,1893
非ポリマー7,06115
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)231.438, 89.255, 123.407
Angle α, β, γ (deg.)90.000, 119.150, 90.000
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 1種, 2分子 AG

#1: タンパク質 HIV-1 clade AE gp120 core


分子量: 38218.242 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: Synthesized
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
株: CNE55 / プラスミド: PVRC8400 / 詳細 (発現宿主): CMV-based vector / 細胞株 (発現宿主): GNTI- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: D7S2G1*PLUS

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抗体 , 2種, 4分子 BHCL

#2: 抗体 VRC-PG05 Fab heavy chain


分子量: 24636.877 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 / 詳細 (発現宿主): CMV-based vector / 細胞株 (発現宿主): GNTI- / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 VRC-PG05 Fab light chain


分子量: 24334.020 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): GNTI- / 発現宿主: Homo sapiens (ヒト)

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糖 , 8種, 22分子

#4: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-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: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-i1_g2-h1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: 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: 合成
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
#6: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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: 1 / 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]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/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)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}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-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-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: 1559.386 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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-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]{}}}}}}LINUCSPDB-CARE
#8: 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-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-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: 1883.668 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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-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]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#9: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-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: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-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: 14 / 由来タイプ: 合成 / 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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非ポリマー , 3種, 184分子

#12: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C2H6O2
#13: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H3O2
#14: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 176 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 3.19 Å3/Da / 溶媒含有率: 61.46 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 9.8% PEG 4000, 0.196 M Sodium acetate, 98 mM Tris/Cl-, pH 8.5 and 0.6% 1,6-hexanediol

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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: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年7月13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: 2.38→50 Å / Num. obs: 77984 / % possible obs: 88.8 % / 冗長度: 3.3 % / Biso Wilson estimate: 49.59 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 1.647 / Net I/σ(I): 10.6 / Num. measured all: 260022
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
2.38-2.422.10.44722070.7030.3460.5690.94550.4
2.42-2.472.20.44825740.6840.3370.5641.10159.2
2.47-2.512.40.40828890.7540.2970.5071.07466.4
2.51-2.562.50.41431520.7760.2910.5081.11372
2.56-2.622.70.40333770.8130.2750.491.20877.1
2.62-2.682.90.39836010.8430.2640.481.17882.6
2.68-2.753.10.35638650.8850.2290.4251.26888.2
2.75-2.823.20.31441820.9130.1980.3721.32195.3
2.82-2.93.50.28842540.9350.1790.341.38798.2
2.9-33.70.24443620.9550.1480.2861.44699
3-3.113.80.20543480.9670.1240.241.64399.1
3.11-3.233.80.16643470.9750.1010.1951.85799.1
3.23-3.383.70.13543110.9820.0830.1591.92699
3.38-3.553.70.11743640.9840.0720.1382.1498.8
3.55-3.783.70.09943290.9880.0610.1172.21798.8
3.78-4.073.60.08443430.990.0520.0992.04298.6
4.07-4.483.60.07243510.9890.0460.0861.91798.5
4.48-5.133.60.06643430.9910.0410.0781.8198.3
5.13-6.463.60.06343900.9920.0390.0741.62598.4
6.46-503.50.05843950.9940.0360.0681.46897.1

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解析

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SERGUIデータ収集
SCALEPACKデータスケーリング
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.22データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4YDL

4ydl


解像度: 2.382→39.847 Å / SU ML: 0.27 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 28.1
Rfactor反射数%反射
Rfree0.2284 3886 4.99 %
Rwork0.1922 --
obs0.194 77824 88.52 %
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: 221.93 Å2 / Biso mean: 90.1428 Å2 / Biso min: 20.31 Å2
精密化ステップサイクル: final / 解像度: 2.382→39.847 Å
タンパク質核酸リガンド溶媒全体
原子数12045 0 903 176 13124
Biso mean--87.3 54.67 -
残基数----1553
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00313310
X-RAY DIFFRACTIONf_angle_d0.67818202
X-RAY DIFFRACTIONf_chiral_restr0.0472217
X-RAY DIFFRACTIONf_plane_restr0.0042215
X-RAY DIFFRACTIONf_dihedral_angle_d14.8018013
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3825-2.41150.2753800.2611404148447
2.4115-2.4420.2948870.25471651173856
2.442-2.47420.2966740.25361818189261
2.4742-2.5080.30831060.25081952205867
2.508-2.54390.28521160.26232088220470
2.5439-2.58180.28841140.26922209232374
2.5818-2.62220.3181070.26652290239777
2.6222-2.66520.37011090.29122408251781
2.6652-2.71110.32321240.27962516264084
2.7111-2.76040.29291220.2582720284290
2.7604-2.81350.29841670.23752796296395
2.8135-2.87090.30161550.23832908306398
2.8709-2.93330.2911480.24242924307299
2.9333-3.00150.24981560.23592929308599
3.0015-3.07650.28361520.24872959311199
3.0765-3.15970.26341460.23212976312299
3.1597-3.25260.2591730.22412913308699
3.2526-3.35760.25661460.20092944309099
3.3576-3.47750.22171650.20192938310399
3.4775-3.61660.2071670.19952961312899
3.6166-3.78110.24791650.19222909307499
3.7811-3.98030.20281600.18122958311899
3.9803-4.22940.19991530.17032956310999
4.2294-4.55550.19271550.14932934308998
4.5555-5.01320.19351500.14612963311398
5.0132-5.73680.17251480.15712950309898
5.7368-7.22070.22721700.18942986315698
7.2207-39.85270.1931710.15622978314997
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)
12.25361.99471.41493.844-0.64151.9633-0.0022-0.5120.75220.57010.120.9065-1.0658-0.8737-0.12041.4590.68420.37141.56190.05881.0454-44.58869.9091.692
22.04181.85370.25492.43160.44960.1102-0.3187-0.5791.3461.75220.54931.1044-1.3713-0.4145-0.25322.13350.68150.25161.27970.14271.1216-34.98679.029-1.913
32.68820.98310.33523.56180.10514.17260.1762-0.34510.03850.9164-0.0025-0.0998-0.64120.202-0.17561.12380.36870.05431.13110.09980.4364-26.9358.812-0.799
45.14243.4061-3.74525.3228-1.61334.0988-0.2972-0.0319-0.5877-1.3012-0.03960.39890.666-0.55910.36740.43460.1517-0.2270.69810.07360.7915-49.70860.316-49.715
54.1187-1.45961.40613.1982-0.43963.8663-0.1439-0.5203-0.40720.14210.26740.762-0.2726-0.5245-0.12050.48450.2490.00210.56280.13450.5888-44.49362.401-39.063
62.942-1.5367-1.08272.45890.79622.19220.25990.8474-1.8848-0.6978-0.64491.7782-0.0606-0.48570.26590.8240.2879-0.55830.817-0.37321.5835-44.39745.402-67.142
70.25661.06950.39786.4082-0.79823.52990.39220.9633-1.83490.52120.24560.77940.2064-1.1682-0.50010.78550.2284-0.4661.1854-0.37342.2697-52.71945.254-66.3
82.88351.33041.01031.16512.14676.5502-0.0832-0.2501-0.3612-0.0894-0.02260.026-0.61410.0040.11540.33790.06680.01540.23340.090.3476-20.27753.346-43.356
95.04220.9265-2.48689.2608-6.18244.8272-0.3796-1.1514-0.39250.44790.3389-0.1905-0.47110.39940.13380.66010.34040.02810.68430.09670.3889-25.01460.261-24.68
108.1429-2.15740.47123.37320.38862.0418-0.01310.3334-0.6388-0.07910.2070.67710.0039-0.6481-0.24410.41160.0605-0.03270.28490.1080.5133-33.04649.825-42.182
119.15410.70011.26018.88816.78247.7512-0.7128-0.6096-1.87041.40350.39630.41170.9459-0.0060.13030.530.20560.12220.52010.3190.7136-29.65145.05-32.354
123.3969-2.05980.43752.98550.22893.26520.15640.4214-0.8724-0.4058-0.11490.76340.1172-0.1649-0.150.38090.0331-0.13040.3171-0.06390.6026-30.45448.427-53.941
135.3088-0.83674.97351.21720.21386.02190.33250.984-0.8544-1.1651-0.7320.4477-0.70810.0270.12431.10930.3397-0.38850.6828-0.30130.8085-28.67645.932-70.455
141.0090.586-0.04920.43-0.60122.6238-0.03671.5556-0.1292-0.97010.00230.5074-0.6484-0.60980.12391.79920.7481-0.9221.5962-0.67920.6379-35.66747.309-83.029
157.1585-1.23365.50210.5777-1.09364.25210.99741.2007-1.195-0.8906-1.07491.03650.6127-0.8406-0.09871.30050.4125-0.32931.5118-0.77991.2328-31.14837.642-81.196
164.3669-3.01-2.24394.89545.04474.97450.2077-0.1433-0.9081.1066-0.61530.67621.3343-0.83130.32330.7555-0.1785-0.00951.01390.06830.5634-33.18416.69832.505
172.6045-1.72830.27636.78781.45866.02-0.02370.3525-1.0850.01250.1493-0.08221.2665-0.3507-0.1440.6412-0.2458-0.00830.7632-0.16710.7647-26.90213.79330.726
189.8646-7.28082.6535.4132-1.75088.59980.0610.4615-1.5229-0.56660.15592.24880.7243-1.1595-0.13580.5211-0.2353-0.03391.1678-0.0590.6657-36.27323.60623.803
198.2761-1.55555.78959.1618-2.12447.8753-0.46260.369-0.8838-1.11460.35720.9417-0.1626-1.39320.13570.7436-0.262-0.23871.64660.31060.9352-45.76938.0216.693
202.6326-1.22091.05647.00330.9984.0061-0.1310.6294-0.59470.12970.4363-0.3860.5763-0.5525-0.28970.409-0.19920.11651.0535-0.13330.599-27.94420.21828.406
212.5643-2.5161-4.74754.11494.20378.88260.00480.2949-1.21780.66150.0497-0.13851.99011.44380.01321.21410.2767-0.13370.878-0.33061.3802-17.4125.66724.549
227.3733-1.67973.55027.79952.81757.52420.20631.0314-1.17321.05950.0075-0.05560.48890.7252-0.21560.37630.050.03720.8129-0.20350.5447-26.17721.21730.116
233.61162.2134-2.60981.96040.34197.8023-0.51191.012-1.1032-0.5940.7193-0.46070.8742-0.0304-0.12550.505-0.10150.14921.2823-0.38860.5853-15.27624.29620.768
240.0421-0.07110.03530.5506-1.21233.068-0.13991.0369-0.3545-0.57570.43460.08271.3128-0.7314-0.29011.049-0.38270.01282.091-0.56650.6605-19.08819.368.376
257.6554-5.9922-2.04895.57114.52239.2403-0.16351.30790.5635-0.4170.3142-0.8455-0.70130.2249-0.14470.3498-0.17870.0141.09120.03640.4468-16.5240.09925.282
262.74631.3304-0.84510.90550.4094.6794-0.66112.0137-0.2541-0.55390.7463-0.1043-0.21650.4563-0.19470.6432-0.29060.14241.8966-0.20870.4043-14.63534.70313.509
270.32441.3317-1.04045.6252-4.38443.4218-0.36470.8878-0.3553-0.43790.23730.2792-1.4537-0.7515-0.17940.6461-0.2295-0.05051.58320.21350.374-28.48941.7921.915
286.88492.3205-3.88926.7206-2.22074.7442-0.00560.30510.3412-0.57890.5248-0.9539-0.97310.5282-0.47690.8613-0.58250.131.86790.06830.4782-10.0439.99612.005
290.8484-0.1229-1.58322.5589-1.02193.4644-0.47041.0251-0.0928-0.86870.39020.6319-0.594-0.8544-0.03270.8669-0.1542-0.13631.83730.3570.2829-28.47140.62716.189
301.448-2.64522.55618.1569-0.72119.2791-0.3448-0.21150.3554-0.10580.01770.891-1.2446-1.46350.29610.6610.0776-0.02331.53510.3350.4728-33.60245.49523.344
310.0686-0.01770.49111.59420.75523.4982-0.47551.8876-0.4256-0.82330.52830.1308-0.1688-0.61010.01020.7751-0.27370.11922.4005-0.50340.1714-16.71729.2410.704
326.26592.8511-1.26212.558-3.98669.3977-0.17191.1764-1.8016-0.76940.4709-1.19080.8789-0.6299-0.38010.6337-0.1650.0031.1428-0.4630.8798-26.1415.28422.438
332.2680.36440.16091.1728-0.17443.4221-0.0527-0.4413-0.05830.1635-0.0680.14-0.2856-0.74210.12730.27970.12880.03160.57520.00660.3097-12.55539.00158.014
343.02330.84760.7637.8722.99942.43880.7449-1.00070.88260.9303-0.60070.8751-1.1493-0.5127-0.09311.2137-0.00610.350.9891-0.23920.6658-1.37860.05778.052
358.11785.95992.5994.77873.44354.47860.05820.2663-0.20240.117-0.0004-0.31-0.23950.2177-0.09580.24830.07440.01680.1997-0.00050.285710.09346.79446.869
365.4530.87655.40230.13680.90035.3406-0.07631.2425-0.567-0.46080.0325-0.0680.05510.4180.07090.31210.02230.07830.5988-0.04720.3261-3.07236.20735.011
379.74541.33030.25026.9935-3.73245.65320.1647-0.3661.00410.09320.13540.4372-1.2528-0.7098-0.24140.30710.1018-0.03640.2088-0.01230.3331-1.7450.78451.278
388.65854.49045.44054.2365.85218.3357-0.10270.72910.7811-0.43790.04330.3533-0.789-0.20320.06260.51120.18270.01110.43430.13150.3246-3.953.06640.26
392.67151.153-0.3382.7355-0.59872.49540.3129-0.64310.39990.6714-0.20490.0872-0.87020.1313-0.04330.524-0.00110.06040.3933-0.10360.28836.35254.43459.661
401.8178-1.58411.9031.477-1.52119.25550.0318-1.09660.80231.2664-0.5324-1.1697-0.08420.66840.38081.0228-0.3275-0.20211.1-0.10150.61219.00561.63771.769
418.82872.65226.01397.59114.31875.01130.7763-2.29490.52332.3134-0.4037-1.22780.78990.361-0.37881.3173-0.3521-0.20291.5018-0.12390.760919.38457.39982.041
428.0461-2.7154.04932.0007-6.73035.08430.1002-0.23150.22620.63170.26170.007-1.2179-0.6587-0.35090.7591-0.0270.08770.5189-0.09180.4378.37162.2761.24
430.17970.06410.27220.30380.38150.60880.4328-1.37110.42831.1698-0.5879-0.3768-0.39460.3396-0.08891.9368-0.7342-0.1271.7745-0.3690.534717.74565.16883.932
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:215 )A44 - 215
2X-RAY DIFFRACTION2( CHAIN A AND RESID 216:258 )A216 - 258
3X-RAY DIFFRACTION3( CHAIN A AND RESID 259:492 )A259 - 492
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:17 )B1 - 17
5X-RAY DIFFRACTION5( CHAIN B AND RESID 18:111 )B18 - 111
6X-RAY DIFFRACTION6( CHAIN B AND RESID 112:193 )B112 - 193
7X-RAY DIFFRACTION7( CHAIN B AND RESID 194:214 )B194 - 214
8X-RAY DIFFRACTION8( CHAIN C AND RESID 1:25 )C1 - 25
9X-RAY DIFFRACTION9( CHAIN C AND RESID 26:32 )C26 - 32
10X-RAY DIFFRACTION10( CHAIN C AND RESID 33:48 )C33 - 48
11X-RAY DIFFRACTION11( CHAIN C AND RESID 49:61 )C49 - 61
12X-RAY DIFFRACTION12( CHAIN C AND RESID 62:137 )C62 - 137
13X-RAY DIFFRACTION13( CHAIN C AND RESID 138:174 )C138 - 174
14X-RAY DIFFRACTION14( CHAIN C AND RESID 175:198 )C175 - 198
15X-RAY DIFFRACTION15( CHAIN C AND RESID 199:214 )C199 - 214
16X-RAY DIFFRACTION16( CHAIN G AND RESID 44:64 )G44 - 64
17X-RAY DIFFRACTION17( CHAIN G AND RESID 65:98 )G65 - 98
18X-RAY DIFFRACTION18( CHAIN G AND RESID 99:115 )G99 - 115
19X-RAY DIFFRACTION19( CHAIN G AND RESID 116:202 )G116 - 202
20X-RAY DIFFRACTION20( CHAIN G AND RESID 203:235 )G203 - 235
21X-RAY DIFFRACTION21( CHAIN G AND RESID 236:245 )G236 - 245
22X-RAY DIFFRACTION22( CHAIN G AND RESID 246:255 )G246 - 255
23X-RAY DIFFRACTION23( CHAIN G AND RESID 256:273 )G256 - 273
24X-RAY DIFFRACTION24( CHAIN G AND RESID 274:287 )G274 - 287
25X-RAY DIFFRACTION25( CHAIN G AND RESID 288:301 )G288 - 301
26X-RAY DIFFRACTION26( CHAIN G AND RESID 324:378 )G324 - 378
27X-RAY DIFFRACTION27( CHAIN G AND RESID 379:385 )G379 - 385
28X-RAY DIFFRACTION28( CHAIN G AND RESID 386:398 )G386 - 398
29X-RAY DIFFRACTION29( CHAIN G AND RESID 399:431 )G399 - 431
30X-RAY DIFFRACTION30( CHAIN G AND RESID 432:444 )G432 - 444
31X-RAY DIFFRACTION31( CHAIN G AND RESID 445:474 )G445 - 474
32X-RAY DIFFRACTION32( CHAIN G AND RESID 475:491 )G475 - 491
33X-RAY DIFFRACTION33( CHAIN H AND RESID 1:109 )H1 - 109
34X-RAY DIFFRACTION34( CHAIN H AND RESID 110:213 )H110 - 213
35X-RAY DIFFRACTION35( CHAIN L AND RESID 1:25 )L1 - 25
36X-RAY DIFFRACTION36( CHAIN L AND RESID 26:32 )L26 - 32
37X-RAY DIFFRACTION37( CHAIN L AND RESID 33:48 )L33 - 48
38X-RAY DIFFRACTION38( CHAIN L AND RESID 49:61 )L49 - 61
39X-RAY DIFFRACTION39( CHAIN L AND RESID 62:137 )L62 - 137
40X-RAY DIFFRACTION40( CHAIN L AND RESID 138:150 )L138 - 150
41X-RAY DIFFRACTION41( CHAIN L AND RESID 151:163 )L151 - 163
42X-RAY DIFFRACTION42( CHAIN L AND RESID 164:174 )L164 - 174
43X-RAY DIFFRACTION43( CHAIN L AND RESID 175:213 )L175 - 213

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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://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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