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- PDB-4fp8: Crystal structure of broadly neutralizing antibody C05 bound to H... -

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基本情報

登録情報
データベース: PDB / ID: 4fp8
タイトルCrystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin, HA1 subunit
要素
  • (Antibody C05, ...) x 2
  • Hemagglutinin HA1 chain
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / viral fusion protein / immunoglobulin / virus attachment and entry / immune recognition / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / membrane
類似検索 - 分子機能
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
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: 2.947 Å
データ登録者Ekiert, D.C. / Wilson, I.A.
引用ジャーナル: Nature / 年: 2012
タイトル: Cross-neutralization of influenza A viruses mediated by a single antibody loop.
著者: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / ...著者: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / Lawrence Horowitz / Andrew B Ward / Peter Palese / Richard Webby / Richard A Lerner / Ramesh R Bhatt / Ian A Wilson /
要旨: Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that ...Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies. Here we report the isolation and characterization of an antibody called C05, which neutralizes strains from multiple subtypes of influenza A virus, including H1, H2 and H3. X-ray and electron microscopy structures show that C05 recognizes conserved elements of the receptor-binding site on the haemagglutinin surface glycoprotein. Recognition of the haemagglutinin receptor-binding site is dominated by a single heavy-chain complementarity-determining region 3 loop, with minor contacts from heavy-chain complementarity-determining region 1, and is sufficient to achieve nanomolar binding with a minimal footprint. Thus, binding predominantly with a single loop can allow antibodies to target small, conserved functional sites on otherwise hypervariable antigens.
履歴
登録2012年6月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年9月19日Provider: repository / タイプ: Initial release
改定 1.12012年10月3日Group: Database references
改定 1.22012年10月10日Group: Database references
改定 2.02019年12月25日Group: Database references / Derived calculations / Polymer sequence
カテゴリ: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
改定 3.02020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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 3.12021年5月19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_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
改定 3.22023年9月13日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 3.32024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

ダウンロードとリンク

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集合体

登録構造単位
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA1 chain
H: Antibody C05, heavy chain
L: Antibody C05, light chain
I: Antibody C05, heavy chain
M: Antibody C05, light chain
J: Antibody C05, heavy chain
N: Antibody C05, light chain
K: Antibody C05, heavy chain
O: Antibody C05, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)319,68123
ポリマ－318,29112
非ポリマー1,39011
水00
1
A: Hemagglutinin HA1 chain
H: Antibody C05, heavy chain
L: Antibody C05, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,9907
ポリマ－79,5733
非ポリマー4174
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Hemagglutinin HA1 chain
I: Antibody C05, heavy chain
M: Antibody C05, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,6384
ポリマ－79,5733
非ポリマー651
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Hemagglutinin HA1 chain
J: Antibody C05, heavy chain
N: Antibody C05, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)80,1937
ポリマ－79,5733
非ポリマー6214
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Hemagglutinin HA1 chain
K: Antibody C05, heavy chain
O: Antibody C05, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,8595
ポリマ－79,5733
非ポリマー2872
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)90.794, 247.720, 95.380
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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抗体 , 2種, 8分子 HIJKLMNO

#2: 抗体
Antibody C05, heavy chain


分子量: 25474.379 Da / 分子数: 4 / 断片: Fab / 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): HEK 293 Freestyle / 発現宿主: Homo sapiens (ヒト)
#3: 抗体
Antibody C05, light chain


分子量: 23367.018 Da / 分子数: 4 / 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): HEK 293 Freestyle / 発現宿主: Homo sapiens (ヒト)

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タンパク質 / 非ポリマー , 2種, 12分子 ABCD

#1: タンパク質
Hemagglutinin HA1 chain / Hemagglutinin receptor binding subunit HA1


分子量: 30731.434 Da / 分子数: 4 / 断片: UNP residues 59-325 / 由来タイプ: 組換発現
由来: (組換発現) Influenza A virus (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): High Five / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q91MA7
#6: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn

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糖 , 2種, 3分子

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


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


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

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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: 3.37 Å3/Da / 溶媒含有率: 63.49 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4.5
詳細: 10% w/v PEG3000, 200 mM zinc acetate, 100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: 1.033 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2010年3月10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: 1.033 Å / 相対比: 1
反射解像度: 2.921→50 Å / Num. obs: 84287 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / 冗長度: 3.1 % / Biso Wilson estimate: 69.9 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.9
反射 シェル解像度: 2.921→3.06 Å / 冗長度: 3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.58 / % possible all: 97.2

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解析

ソフトウェア
名称バージョン分類
Blu-IceEpicsデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.7.2_869)精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 4FNK AND 4FNL

4fnk

4fnl


解像度: 2.947→44.495 Å / SU ML: 0.77 / σ(F): 0 / 位相誤差: 23.66 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.241 4191 4.98 %RANDOM
Rwork0.2122 ---
obs0.2136 84209 95.1 %-
溶媒の処理減衰半径: 0.98 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 24.708 Å2 / ksol: 0.299 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--2.6741 Å2-0 Å2-0.9601 Å2
2--0.111 Å20 Å2
3---2.5631 Å2
精密化ステップサイクル: LAST / 解像度: 2.947→44.495 Å
タンパク質核酸リガンド溶媒全体
原子数21913 0 64 0 21977
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00522984
X-RAY DIFFRACTIONf_angle_d1.10431281
X-RAY DIFFRACTIONf_dihedral_angle_d13.7058340
X-RAY DIFFRACTIONf_chiral_restr0.0673482
X-RAY DIFFRACTIONf_plane_restr0.0064069
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.947-2.980.38011230.33872435X-RAY DIFFRACTION87
2.98-3.0150.31681270.32082693X-RAY DIFFRACTION97
3.015-3.05180.35421590.30142730X-RAY DIFFRACTION97
3.0518-3.09040.34131460.2942710X-RAY DIFFRACTION97
3.0904-3.13110.28831500.2782698X-RAY DIFFRACTION97
3.1311-3.17390.27411500.27562739X-RAY DIFFRACTION97
3.1739-3.21930.28611310.26512645X-RAY DIFFRACTION96
3.2193-3.26730.2861340.27092758X-RAY DIFFRACTION97
3.2673-3.31840.33191450.26232674X-RAY DIFFRACTION97
3.3184-3.37270.28741290.25482726X-RAY DIFFRACTION96
3.3727-3.43090.28681440.24962709X-RAY DIFFRACTION97
3.4309-3.49320.24371280.23372730X-RAY DIFFRACTION96
3.4932-3.56040.24751510.23512650X-RAY DIFFRACTION96
3.5604-3.6330.28451350.23062731X-RAY DIFFRACTION96
3.633-3.7120.24611490.22992648X-RAY DIFFRACTION96
3.712-3.79830.25361580.22612701X-RAY DIFFRACTION96
3.7983-3.89320.2391170.21752662X-RAY DIFFRACTION96
3.8932-3.99840.22411490.20972714X-RAY DIFFRACTION96
3.9984-4.1160.24951420.18682654X-RAY DIFFRACTION95
4.116-4.24880.20261160.18672672X-RAY DIFFRACTION95
4.2488-4.40050.22441350.17922685X-RAY DIFFRACTION95
4.4005-4.57650.19531600.16622649X-RAY DIFFRACTION95
4.5765-4.78460.17751380.15512676X-RAY DIFFRACTION95
4.7846-5.03650.18281380.16252658X-RAY DIFFRACTION95
5.0365-5.35160.19381500.17332632X-RAY DIFFRACTION94
5.3516-5.7640.2481580.19042598X-RAY DIFFRACTION94
5.764-6.34250.25931560.2052626X-RAY DIFFRACTION93
6.3425-7.25690.23461110.21472638X-RAY DIFFRACTION93
7.2569-9.12990.21551270.18542619X-RAY DIFFRACTION92
9.1299-44.49960.21341350.19382558X-RAY DIFFRACTION90
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)
10.35541.08350.11564.0020.07271.97570.11680.321-0.977-0.63710.05780.12750.5131-0.0558-0.07340.7984-0.2264-0.21731.0613-0.43541.3884-116.4562-111.012831.357
21.88560.89691.61962.77240.04663.1461-0.13120.6511-0.1175-0.15630.12260.05280.05180.1310.10560.4804-0.0247-0.00330.4743-0.10240.727-98.2296-101.297940.9748
32.9037-0.70841.89880.1947-0.4341.2941-0.29440.0103-0.35530.04860.0750.25580.0006-0.336-0.01430.53810.02910.04090.4914-0.08070.6778-98.0386-105.353543.4344
42.6131-0.106-0.40672.5835-0.00480.9895-0.2663-0.1251-0.46130.18190.00910.35960.0534-0.1052-0.00380.46610.01080.08690.31980.08260.4982-96.8446-97.69354.6941
56.3995-0.1314-0.00534.9240.5253.354-0.17490.149-0.1870.1535-0.0447-0.3621-0.23020.2195-0.00280.3796-0.04660.01930.2890.01390.4474-83.6077-94.86953.076
66.744-0.903-0.94332.37850.24831.2015-0.3149-0.7977-0.30410.39640.17690.2317-0.1379-0.01010.07820.51910.09140.09930.3790.12320.3832-98.4504-97.262862.7042
71.47010.17060.87956.67260.11831.112-0.2698-0.4959-0.41060.39880.0033-0.86120.41570.65050.31110.47820.0333-0.10840.56270.23940.7071-75.5205-103.246861.652
83.0569-1.9592-0.39976.38731.61024.4981-0.4302-0.2399-0.93680.47190.23810.04020.3922-0.2150.62490.42950.022-0.02380.47120.15250.5691-87.4305-107.51160.0495
92.2393-0.2417-0.47072.7050.59281.95470.0785-0.3867-0.50480.27380.15970.12630.1034-0.25340.22410.45730.02860.06240.40330.18290.4386-97.0504-102.552562.5764
102.03960.3669-0.46992.80351.61333.1938-0.16730.2594-0.66280.0106-0.35220.6105-0.0456-0.4998-0.45370.41430.01710.06890.441-0.01470.5962-102.8291-102.95949.3118
115.6402-1.54720.26562.79291.19270.9658-0.59580.0254-0.1717-0.16050.4251.4640.2606-1.1150.09120.6676-0.2046-0.0681.2124-0.3371.5009-118.9452-113.483732.2799
120.51570.66020.50372.70841.07450.5912-0.00370.0191-0.4709-0.09580.0073-0.01380.3019-0.1992-0.04170.824-0.4410.15340.9325-0.36251.729-117.0172-120.211538.4751
136.9637-4.8738-0.5818.73640.04163.44590.01610.9784-0.4249-1.1720.1223-0.5745-0.02580.7788-0.03841.4669-0.05950.30321.7669-0.25420.985314.7858-49.798225.7545
144.59291.2205-0.33793.92411.23025.92270.24561.00870.1264-0.11370.2354-0.9001-0.16970.4649-0.59570.5233-0.10360.01720.78240.02480.62065.9361-39.694644.0541
152.01180.0711-0.43991.8060.12535.7671-0.37531.28080.2692-0.35410.3075-0.1491-0.160.39380.06320.4614-0.10960.03020.8343-0.00310.49693.235-43.601744.3345
164.3013-4.1372-2.13638.24464.81686.5106-0.01281.48070.4414-1.4181-0.3592-0.3747-0.40710.07430.38630.5843-0.1576-0.0690.8210.09970.4323-4.231-41.138938.4423
175.9218-2.7374-1.95075.05040.38084.84490.0026-0.00751.2734-0.20020.04860.1203-0.51490.1606-0.06820.5296-0.0354-0.07470.2368-0.0380.6103-7.6137-31.026657.5709
184.6828-0.8054-1.22533.3141-0.41197.6272-0.16670.3630.4064-0.46120.0640.6647-0.2994-0.48630.04340.4038-0.1038-0.12060.2758-0.01780.5831-14.9623-37.078653.7984
195.3234-0.7582-0.25233.8464-1.10954.39690.410.2944-0.6541-0.49470.17050.69450.2815-0.255-0.59950.4205-0.057-0.12660.3151-0.07940.5763-13.1581-44.894455.1573
203.7758-1.0719-0.51563.64850.44722.61930.01051.26470.1187-0.7244-0.07320.3211-0.19510.20070.02730.5311-0.0923-0.11940.6903-0.03110.4563-7.9999-40.512842.0735
212.9713-1.4098-2.11272.2255-0.72967.067-0.44181.1681-0.3429-1.09550.2146-0.17960.02520.39320.11451.33850.02240.28961.8527-0.41220.886713.7804-52.290723.2724
220.1699-0.1561-0.34010.42980.59610.9613-0.13610.2128-0.1581-0.62630.1982-0.13180.17050.1505-0.15111.70350.1454-0.14551.674-0.76530.91087.3284-58.857325.2584
239.7675-0.558-0.10220.0690.19630.98650.2589-0.74120.71670.54020.21021.71930.9552-1.0058-0.4481.0658-0.24510.38431.96420.04581.77332.5649-51.023589.8973
243.6075-0.6289-0.13182.502-0.6213.3785-0.1272-0.27260.14740.21330.2007-0.2865-0.10370.0043-0.0720.34770.0158-0.0420.385-0.0760.515926.2969-45.993266.1041
255.33050.49720.17823.8763-0.00782.0108-0.24-0.8832-0.23760.5570.1498-0.22820.1058-0.2960.09020.40570.092-0.05930.5771-0.03320.516427.1154-49.348674.4379
260.6061-0.13221.39450.0326-0.32083.29090.08660.1107-0.9292-0.3138-0.3611-0.45881.77670.40960.24012.30010.19090.60852.33620.15041.43682.4338-54.811492.2634
279.13186.72291.46864.94921.0810.2359-0.26470.2912-0.131-0.083-0.006-0.22940.3817-0.13380.36832.3231-0.6701-0.25592.46130.90991.96866.1867-62.512589.1084
280.754-0.8526-2.0841.0232.42345.8381-0.06790.1202-0.5871-0.7197-0.22320.24750.3178-0.50870.28891.40160.07710.13022.89350.2871.56-40.110410.642450.7833
292.92460.5485-1.2662.1558-1.12133.1540.11180.46760.21570.11840.23260.36-0.4372-0.6435-0.26320.45570.0740.10530.43470.10060.4905-17.196217.070175.0781
300.9276-0.0625-1.56723.09740.3622.74340.1010.92990.13240.07470.23780.648-0.0956-1.296-0.2250.48310.02410.07430.80730.18440.5504-25.410713.696475.6624
314.1199-1.9526-0.42541.19461.02482.5617-0.4366-0.176-0.56890.152-0.53260.31240.3688-0.57020.86081.9166-1.0707-0.52933.68940.04452.8134-42.18477.268450.564
320.0230.0019-0.00840-0.00080.00290.03410.6740.2609-0.87760.4509-1.1835-0.67591.1099-0.41453.2842-1.1958-0.07123.1632-0.46172.6737-39.1838-1.038354.8025
332.67870.6924-0.3015.0940.12230.1231-0.23150.4589-0.6594-0.17930.1121-0.04980.35350.37760.12050.5115-0.0103-0.11270.5834-0.15330.4725-56.2734-88.804145.921
342.35931.1634-0.74341.6765-0.39821.0987-0.17820.4610.384-0.35980.35160.38180.0980.10230.00480.4237-0.1056-0.07650.5490.01920.466-60.3699-82.008744.7057
356.0511-0.2686-2.44216.1812-4.07183.8187-0.1055-1.02510.27291.0966-0.04-0.9431-0.80741.49630.12990.4842-0.0416-0.00280.6161-0.17450.7328-19.3465-72.724459.3349
361.9633-0.37780.55293.407-1.09193.6598-0.3350.1352-0.4271-0.1969-0.0483-0.27280.6336-0.1255-0.12970.4255-0.04930.07150.3667-0.06120.5081-28.6497-78.640452.4482
372.66030.52350.83952.87380.04964.1544-0.0415-0.3504-0.02860.31070.3153-0.60750.53350.53-0.23660.40890.1001-0.04070.4371-0.15590.60341.0567-23.054486.1985
383.3856-0.81961.97782.67342.13425.36650.14570.3632-0.20.09250.5303-0.97080.07121.2881-0.52430.3718-0.01620.00040.5974-0.2590.76426.496-21.286679.1018
390.8090.21710.91311.2201-0.25221.6727-0.2205-0.24590.129-0.04740.5244-0.5449-0.28820.4648-0.20180.34620.0224-0.03230.5047-0.24910.65691.3255-19.985383.181
408.01993.53863.55937.4041-0.10053.1384-0.868-1.74960.95010.89020.93771.725-1.0189-1.6290.03341.0230.40520.10460.98120.36520.8742-13.5251-11.498121.1033
412.6242-1.22541.15642.5450.77153.2401-0.0347-0.2933-1.18730.25880.6090.05620.85260.0304-0.4370.64750.073-0.23660.4121-0.03241.0448-7.552-15.2898111.3621
425.0031-3.0616-3.68584.79911.23586.4831-0.478-0.3199-2.06030.15960.43520.07911.68230.4320.150.8250.2091-0.25060.6432-0.10541.4063-0.5463-22.4273112.4866
431.34322.503-0.54455.7503-3.5536.2514-0.00330.19670.1088-0.6460.07470.46620.5558-0.2607-0.04170.3622-0.02330.0150.67880.13740.603824.3838-26.396333.0271
445.96082.0228-0.16269.4187-1.55416.05060.0212-0.14370.25270.1147-0.30460.4692-0.4458-0.11490.24040.37710.07390.08070.61170.03590.648924.5082-18.563540.5246
452.2766-1.09480.22573.9553-4.02614.4726-0.04230.14850.42870.22750.04050.3873-0.2712-0.27080.04820.40180.0044-0.00120.56250.05960.772124.3635-21.941937.9984
460.23771.3174-0.66527.9339-3.56011.90320.29710.3610.33980.889-0.3124-0.3636-0.52350.53410.06090.40450.01330.09020.60310.18920.588131.8458-29.007146.922
471.08240.993-0.88421.0242-1.18152.03450.08670.36710.4119-0.2391-0.43930.2414-0.3367-0.01150.41380.57990.1079-0.14590.73550.15330.858723.8061-12.400521.2982
480.5425-0.64771.41242.6898-2.23833.83420.59521.95251.4326-0.9004-0.7273-2.1853-0.08211.68310.22040.7769-0.0950.19891.25060.03781.365943.4913-17.3338-0.5692
494.2908-0.7421-0.8254.1012-0.50612.9701-0.16770.0733-1.2267-0.43670.3731-0.16270.5629-0.1544-0.11840.4782-0.0839-0.07090.72810.06831.097136.6236-18.36969.2177
501.6735-0.2325-1.62333.30760.01952.788-0.25720.277-0.7103-0.28080.5350.84910.828-0.9422-0.26650.6513-0.103-0.07531.10780.15461.224327.1877-21.65228.3602
512.23570.5170.34730.82990.38090.24050.4058-0.1484-0.10881.0497-0.611-0.3094-0.96770.78640.09381.0647-0.4305-0.02480.66050.12020.40899.531741.098873.0561
521.121-1.03960.47091.0771-0.87161.98240.42650.02240.66320.387-0.5318-0.5869-0.53381.36220.3491.4379-0.9514-0.22071.63370.36630.881926.87150.650376.4407
530.9368-2.73422.02328.0735-5.9724.41640.5672-0.357-0.50260.25820.2132-0.10541.3797-0.5393-0.67872.3246-1.1894-0.64223.85330.82372.354546.461955.941392.3887
540.391-0.75290.01181.86560.63051.0318-0.1854-0.5782-0.2950.7578-0.3299-0.36060.81720.66490.6711.6925-0.539-0.0653.16311.20361.707436.700347.453684.8569
551.94151.7089-1.00535.40234.34977.54620.1051-0.6636-0.64050.5594-0.6538-1.25671.53592.24190.53692.1752-1.0275-0.6252.820.92581.45435.011557.549284.2799
569.03283.30156.65329.23554.27135.35830.03611.30290.3501-1.5335-0.1910.1846-1.44740.10330.23942.145-0.223-0.35192.6284-0.1381.77752.747245.246395.6814
574.6436-0.82111.16374.1814-1.69824.08310.54170.21910.2662-0.15830.1552-0.1826-0.1712-0.8293-0.66371.94810.0185-0.13432.53460.6751.325942.64447.223378.6533
588.9458-0.55343.08864.8197-0.35713.51490.1001-0.22570.53030.2142-0.00330.8235-0.0167-0.12530.32570.2970.00360.08740.5013-0.04520.6588-58.3188-64.613865.5663
591.95721.33830.63961.3524-0.21982.2261-0.1576-0.42650.9362-0.01180.01090.8144-0.2417-0.65480.61950.30980.04460.08860.5195-0.10560.9525-69.9175-67.623861.583
606.232-1.3011-2.00877.65630.17852.1470.1684-0.4404-0.5310.35190.0928-0.33020.49940.43330.2060.467-0.0222-0.00880.52530.01140.41-59.5507-78.529164.5621
612.5666-0.0760.65742.6954-0.26695.12280.0318-0.35520.21120.6308-0.03110.41120.1514-0.0135-0.06370.42440.03810.08520.4376-0.10360.5784-59.8678-71.114466.9467
621.67560.3221-0.20591.01980.42310.6591-0.2744-0.24720.42610.00390.17520.26240.0988-0.05390.02330.3445-0.0066-0.04520.4118-0.06710.431-45.0629-68.266760.7145
633.68430.9166-2.2611.7903-1.7524.4261-0.16410.05960.3532-0.08130.17850.0863-0.161-0.02420.10470.33640.0016-0.11480.3459-0.07940.4798-25.52-61.654154.4323
642.55580.2338-2.06922.12120.08813.9851-0.0512-0.23880.13380.09720.2-0.4265-0.03990.21140.08390.3520.0159-0.09180.3937-0.12540.5087-24.8544-62.161558.0107
654.4115-1.8186-1.13314.54772.30336.26530.01260.24290.0042-0.3710.08370.0520.0277-0.2486-0.14190.3345-0.0579-0.02340.26910.0060.38-15.3596-8.401679.297
660.9219-0.24520.04931.57911.04253.93830.0577-0.0471-0.198-0.00620.1214-0.10680.1248-0.1756-0.16240.294-0.01840.00050.2550.04260.5001-13.3675-6.323895.9817
676.79212.05684.70244.28772.72618.1614-0.3275-0.21180.13570.17310.38140.2702-0.26760.3717-0.00020.36970.01960.09150.3126-0.02720.5051-10.29990.735111.5652
684.83930.53712.09592.39870.63415.7697-0.1365-1.41510.00080.50480.0599-0.0793-0.0098-0.02460.07980.56080.0530.02140.7570.030.3906-10.06412.2777123.7366
695.6091.3376-1.61151.6009-0.76632.3674-0.0496-0.26490.19810.3223-0.3884-0.4436-0.2610.94920.32670.4692-0.0512-0.08880.92620.2530.8347.9009-18.538640.4332
701.21980.5099-1.76481.0171-1.20812.8730.0220.0145-0.14010.0059-0.09770.0605-0.26460.08780.00590.3616-0.0948-0.00060.7427-0.00250.75443.6768-12.028716.2208
716.7953-5.11045.41596.8907-3.37386.319-0.1650.23670.1047-0.0081-0.195-0.3609-0.3334-0.09430.33730.3428-0.08940.13930.79320.06960.764646.0696-5.2979.3412
724.5672-1.09081.33663.9314-0.49024.11770.25511.33260.157-0.4666-0.06570.162-0.4795-0.3733-0.16410.5442-0.09090.03021.2940.12170.641346.3684-3.339-2.7411
730.2727-0.0159-0.3230.3389-0.19490.53670.0988-0.61220.09541.0745-0.2384-0.0696-0.89320.5594-0.11292.4914-0.83880.26891.25960.06180.42816.509746.423394.7446
740.1078-0.12660.28240.1564-0.3420.7363-0.3170.62280.47370.031-0.4909-0.543-1.17531.17670.49792.2773-1.113-0.77283.01240.64551.358636.978559.233894.6077
750.9719-0.3164-0.52980.62380.41060.56410.1792-0.64060.32160.28850.3788-0.64730.13070.2631-0.29442.5656-1.2138-0.96032.3970.26832.062938.213471.378592.597
760.4519-0.35030.67290.3954-0.42892.739-0.19720.30610.33340.2071-0.147-0.3358-0.31510.43080.2642.7421-1.3744-1.03612.4690.84131.711733.73857.763993.4915
772.7661-0.9966-1.3980.37990.49890.72690.23110.3121-0.5514-0.57310.02440.48430.7261-1.0668-0.20372.1529-0.3554-0.39312.20880.69772.781550.337873.461486.7953
788.70030.9402-7.86140.1034-0.85487.1060.05120.30170.20370.2206-0.39980.0797-0.0139-0.08820.27922.5022-1.127-0.69463.41490.47891.817842.773467.0562101.0272
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resseq 43:57 )A43 - 57
2X-RAY DIFFRACTION2chain A and ( resseq 58:79 )A58 - 79
3X-RAY DIFFRACTION3chain A and ( resseq 80:104 )A80 - 104
4X-RAY DIFFRACTION4chain A and ( resseq 105:136 )A105 - 136
5X-RAY DIFFRACTION5chain A and ( resseq 137:163 )A137 - 163
6X-RAY DIFFRACTION6chain A and ( resseq 164:184 )A164 - 184
7X-RAY DIFFRACTION7chain A and ( resseq 185:201 )A185 - 201
8X-RAY DIFFRACTION8chain A and ( resseq 202:228 )A202 - 228
9X-RAY DIFFRACTION9chain A and ( resseq 229:247 )A229 - 247
10X-RAY DIFFRACTION10chain A and ( resseq 248:274 )A248 - 274
11X-RAY DIFFRACTION11chain A and ( resseq 275:294 )A275 - 294
12X-RAY DIFFRACTION12chain A and ( resseq 295:309 )A295 - 309
13X-RAY DIFFRACTION13chain B and ( resseq 43:57 )B43 - 57
14X-RAY DIFFRACTION14chain B and ( resseq 58:79 )B58 - 79
15X-RAY DIFFRACTION15chain B and ( resseq 80:104 )B80 - 104
16X-RAY DIFFRACTION16chain B and ( resseq 105:122 )B105 - 122
17X-RAY DIFFRACTION17chain B and ( resseq 123:163 )B123 - 163
18X-RAY DIFFRACTION18chain B and ( resseq 164:201 )B164 - 201
19X-RAY DIFFRACTION19chain B and ( resseq 202:228 )B202 - 228
20X-RAY DIFFRACTION20chain B and ( resseq 229:274 )B229 - 274
21X-RAY DIFFRACTION21chain B and ( resseq 275:294 )B275 - 294
22X-RAY DIFFRACTION22chain B and ( resseq 295:309 )B295 - 309
23X-RAY DIFFRACTION23chain C and ( resseq 44:57 )C44 - 57
24X-RAY DIFFRACTION24chain C and ( resseq 58:228 )C58 - 228
25X-RAY DIFFRACTION25chain C and ( resseq 229:274 )C229 - 274
26X-RAY DIFFRACTION26chain C and ( resseq 275:294 )C275 - 294
27X-RAY DIFFRACTION27chain C and ( resseq 295:308 )C295 - 308
28X-RAY DIFFRACTION28chain D and ( resseq 44:57 )D44 - 57
29X-RAY DIFFRACTION29chain D and ( resseq 58:228 )D58 - 228
30X-RAY DIFFRACTION30chain D and ( resseq 229:274 )D229 - 274
31X-RAY DIFFRACTION31chain D and ( resseq 275:294 )D275 - 294
32X-RAY DIFFRACTION32chain D and ( resseq 295:309 )D295 - 309
33X-RAY DIFFRACTION33chain H and ( resseq 2:35C )H2 - 35
34X-RAY DIFFRACTION34chain H and ( resseq 35D:119 )H35 - 119
35X-RAY DIFFRACTION35chain H and ( resseq 120:139 )H120 - 139
36X-RAY DIFFRACTION36chain H and ( resseq 140:213 )H140 - 213
37X-RAY DIFFRACTION37chain I and ( resseq 2:44 )I2 - 44
38X-RAY DIFFRACTION38chain I and ( resseq 45:82 )I45 - 82
39X-RAY DIFFRACTION39chain I and ( resseq 83:119 )I83 - 119
40X-RAY DIFFRACTION40chain I and ( resseq 120:139 )I120 - 139
41X-RAY DIFFRACTION41chain I and ( resseq 140:198 )I140 - 198
42X-RAY DIFFRACTION42chain I and ( resseq 199:212 )I199 - 212
43X-RAY DIFFRACTION43chain J and ( resseq 2:35C )J2 - 35
44X-RAY DIFFRACTION44chain J and ( resseq 35D:75 )J35 - 75
45X-RAY DIFFRACTION45chain J and ( resseq 76:100E )J76 - 100
46X-RAY DIFFRACTION46chain J and ( resseq 100F:103 )J100 - 103
47X-RAY DIFFRACTION47chain J and ( resseq 104:119 )J104 - 119
48X-RAY DIFFRACTION48chain J and ( resseq 120:139 )J120 - 139
49X-RAY DIFFRACTION49chain J and ( resseq 140:198 )J140 - 198
50X-RAY DIFFRACTION50chain J and ( resseq 199:212 )J199 - 212
51X-RAY DIFFRACTION51chain K and ( resseq 2:100O )K2 - 100
52X-RAY DIFFRACTION52chain K and ( resseq 100P:124 )K100 - 124
53X-RAY DIFFRACTION53chain K and ( resseq 125:144 )K125 - 144
54X-RAY DIFFRACTION54chain K and ( resseq 145:164 )K145 - 164
55X-RAY DIFFRACTION55chain K and ( resseq 165:184 )K165 - 184
56X-RAY DIFFRACTION56chain K and ( resseq 185:193 )K185 - 193
57X-RAY DIFFRACTION57chain K and ( resseq 194:212 )K194 - 212
58X-RAY DIFFRACTION58chain L and ( resseq 1:18 )L1 - 18
59X-RAY DIFFRACTION59chain L and ( resseq 19:32 )L19 - 32
60X-RAY DIFFRACTION60chain L and ( resseq 33:61 )L33 - 61
61X-RAY DIFFRACTION61chain L and ( resseq 62:90 )L62 - 90
62X-RAY DIFFRACTION62chain L and ( resseq 91:121 )L91 - 121
63X-RAY DIFFRACTION63chain L and ( resseq 122:161 )L122 - 161
64X-RAY DIFFRACTION64chain L and ( resseq 162:212 )L162 - 212
65X-RAY DIFFRACTION65chain M and ( resseq 1:61 )M1 - 61
66X-RAY DIFFRACTION66chain M and ( resseq 62:141 )M62 - 141
67X-RAY DIFFRACTION67chain M and ( resseq 142:181 )M142 - 181
68X-RAY DIFFRACTION68chain M and ( resseq 182:212 )M182 - 212
69X-RAY DIFFRACTION69chain N and ( resseq 1:90 )N1 - 90
70X-RAY DIFFRACTION70chain N and ( resseq 91:141 )N91 - 141
71X-RAY DIFFRACTION71chain N and ( resseq 142:181 )N142 - 181
72X-RAY DIFFRACTION72chain N and ( resseq 182:212 )N182 - 212
73X-RAY DIFFRACTION73chain O and ( resseq 1:101 )O1 - 101
74X-RAY DIFFRACTION74chain O and ( resseq 102:143 )O102 - 143
75X-RAY DIFFRACTION75chain O and ( resseq 144:163 )O144 - 163
76X-RAY DIFFRACTION76chain O and ( resseq 164:183 )O164 - 183
77X-RAY DIFFRACTION77chain O and ( resseq 184:193 )O184 - 193
78X-RAY DIFFRACTION78chain O and ( resseq 194:212 )O194 - 212

+
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

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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

他の情報も見る