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- PDB-5i8h: Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer i... -

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基本情報

登録情報
データベース: PDB / ID: 5i8h
タイトルCrystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab
要素
  • (BG505 SOSIP.664 ...) x 2
  • (VRC34.01 Fab ...) x 2
  • PGT122 Fab heavy chain
  • PGT122 Fab light chain
キーワードIMMUNE SYSTEM / HIV-1 / envelope / trimer / fusion peptide / antibody / neutralizing
機能・相同性
機能・相同性情報


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 / viral envelope / virion attachment to host cell / host cell plasma membrane ...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 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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
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: 4.301 Å
データ登録者Xu, K. / Zhou, T. / Kwong, P.D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 米国
引用ジャーナル: Science / 年: 2016
タイトル: Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.
著者: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi ...著者: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi / Gwo-Yu Chuang / Nicole A Doria-Rose / Aliaksandr Druz / Ivelin S Georgiev / Jason Gorman / Jinghe Huang / M Gordon Joyce / Mark K Louder / Xiaochu Ma / Krisha McKee / Sijy O'Dell / Marie Pancera / Yongping Yang / Scott C Blanchard / Walther Mothes / Dennis R Burton / Wayne C Koff / Mark Connors / Andrew B Ward / Peter D Kwong / John R Mascola /
要旨: The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the ...The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.
履歴
登録2016年2月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年5月25日Provider: repository / タイプ: Initial release
改定 1.12016年6月1日Group: Derived calculations
改定 1.22017年9月20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 1.32019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.12024年11月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

ダウンロードとリンク

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集合体

登録構造単位
A: BG505 SOSIP.664 gp120
B: BG505 SOSIP.664 gp41
C: BG505 SOSIP.664 gp120
L: PGT122 Fab light chain
E: VRC34.01 Fab heavy chain
F: VRC34.01 Fab light chain
G: VRC34.01 Fab heavy chain
D: BG505 SOSIP.664 gp41
H: VRC34.01 Fab light chain
I: PGT122 Fab heavy chain
J: PGT122 Fab light chain
K: PGT122 Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)354,77455
ポリマ－332,31812
非ポリマー22,45743
水00
1
A: BG505 SOSIP.664 gp120
B: BG505 SOSIP.664 gp41
E: VRC34.01 Fab heavy chain
F: VRC34.01 Fab light chain
I: PGT122 Fab heavy chain
J: PGT122 Fab light chain
ヘテロ分子

A: BG505 SOSIP.664 gp120
B: BG505 SOSIP.664 gp41
E: VRC34.01 Fab heavy chain
F: VRC34.01 Fab light chain
I: PGT122 Fab heavy chain
J: PGT122 Fab light chain
ヘテロ分子

A: BG505 SOSIP.664 gp120
B: BG505 SOSIP.664 gp41
E: VRC34.01 Fab heavy chain
F: VRC34.01 Fab light chain
I: PGT122 Fab heavy chain
J: PGT122 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)533,28484
ポリマ－498,47618
非ポリマー34,80866
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
C: BG505 SOSIP.664 gp120
L: PGT122 Fab light chain
G: VRC34.01 Fab heavy chain
D: BG505 SOSIP.664 gp41
H: VRC34.01 Fab light chain
K: PGT122 Fab heavy chain
ヘテロ分子

C: BG505 SOSIP.664 gp120
L: PGT122 Fab light chain
G: VRC34.01 Fab heavy chain
D: BG505 SOSIP.664 gp41
H: VRC34.01 Fab light chain
K: PGT122 Fab heavy chain
ヘテロ分子

C: BG505 SOSIP.664 gp120
L: PGT122 Fab light chain
G: VRC34.01 Fab heavy chain
D: BG505 SOSIP.664 gp41
H: VRC34.01 Fab light chain
K: PGT122 Fab heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)531,03881
ポリマ－498,47618
非ポリマー32,56263
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
単位格子
Length a, b, c (Å)252.296, 252.296, 561.202
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 31:141 or resseq 150:184 or resseq...
21(chain C and (resseq 31:141 or resseq 150:184 or resseq...
12chain L
22chain J
13(chain B and (resseq 512:519 or resseq 521:547 or resseq 569:664))
23(chain D and (resseq 512:519 or resseq 521:547 or resseq 569:664))
14chain G or chain H
24chain E or chain F
15chain K
25chain I

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 31:141 or resseq 150:184 or resseq...A31 - 141
121(chain A and (resseq 31:141 or resseq 150:184 or resseq...A150 - 184
131(chain A and (resseq 31:141 or resseq 150:184 or resseq...A190 - 309
141(chain A and (resseq 31:141 or resseq 150:184 or resseq...A312 - 320
151(chain A and (resseq 31:141 or resseq 150:184 or resseq...A321
161(chain A and (resseq 31:141 or resseq 150:184 or resseq...A321
171(chain A and (resseq 31:141 or resseq 150:184 or resseq...A322 - 398
181(chain A and (resseq 31:141 or resseq 150:184 or resseq...A411 - 504
191(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1088 - 1092
1101(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1133
1111(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1137
1121(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1157 - 1161
1131(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1169
1141(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1197 - 1198
1151(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1234 - 1235
1161(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1262 - 1265
1171(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1268 - 1269
1181(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1276
1191(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1295 - 1296
1201(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1301 - 1302
1211(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1331 - 1340
1221(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1355
1231(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1363 - 1364
1241(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1386 - 1387
1251(chain A and (resseq 31:141 or resseq 150:184 or resseq...A1392 - 1393
211(chain C and (resseq 31:141 or resseq 150:184 or resseq...C31 - 141
221(chain C and (resseq 31:141 or resseq 150:184 or resseq...C150 - 184
231(chain C and (resseq 31:141 or resseq 150:184 or resseq...C190 - 309
241(chain C and (resseq 31:141 or resseq 150:184 or resseq...C312 - 320
251(chain C and (resseq 31:141 or resseq 150:184 or resseq...C321
261(chain C and (resseq 31:141 or resseq 150:184 or resseq...C321
271(chain C and (resseq 31:141 or resseq 150:184 or resseq...C322 - 398
281(chain C and (resseq 31:141 or resseq 150:184 or resseq...C411 - 504
291(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1088 - 1092
2101(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1133
2111(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1137
2121(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1157 - 1161
2131(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1169
2141(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1197 - 1198
2151(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1234 - 1235
2161(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1262 - 1265
2171(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1268 - 1269
2181(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1276
2191(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1295 - 1296
2201(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1301 - 1302
2211(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1331 - 1340
2221(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1355
2231(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1363 - 1364
2241(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1386 - 1387
2251(chain C and (resseq 31:141 or resseq 150:184 or resseq...C1392 - 1393
112chain LL6 - 210
212chain JJ6 - 210
113(chain B and (resseq 512:519 or resseq 521:547 or resseq 569:664))B512 - 519
123(chain B and (resseq 512:519 or resseq 521:547 or resseq 569:664))B521 - 547
133(chain B and (resseq 512:519 or resseq 521:547 or resseq 569:664))B569 - 664
213(chain D and (resseq 512:519 or resseq 521:547 or resseq 569:664))D512 - 519
223(chain D and (resseq 512:519 or resseq 521:547 or resseq 569:664))D521 - 547
233(chain D and (resseq 512:519 or resseq 521:547 or resseq 569:664))D569 - 664
114chain G or chain HG1 - 214
124chain G or chain HH1 - 212
214chain E or chain FE1 - 214
224chain E or chain FF1 - 212
115chain KK1 - 211
215chain II1 - 211

NCSアンサンブル:
ID
1
2
3
4
5

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要素

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BG505 SOSIP.664 ... , 2種, 4分子 ACBD

#1: タンパク質 BG505 SOSIP.664 gp120 / Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13- ...Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13-1 Env polyprotein / Endogenous retrovirus group K member 18 Env polyprotein / Endogenous retrovirus group K member 19 Env polyprotein / Endogenous retrovirus group K member 21 Env polyprotein / Endogenous retrovirus group K member 24 Env polyprotein / Endogenous retrovirus group K member 25 Env polyprotein / Endogenous retrovirus group K member 6 Env polyprotein / Endogenous retrovirus group K member 8 Env polyprotein / Endogenous retrovirus group K member 9 Env polyprotein


分子量: 54064.277 Da / 分子数: 2 / 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 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6
#2: タンパク質 BG505 SOSIP.664 gp41 / Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13- ...Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13-1 Env polyprotein / Endogenous retrovirus group K member 18 Env polyprotein / Endogenous retrovirus group K member 19 Env polyprotein / Endogenous retrovirus group K member 21 Env polyprotein / Endogenous retrovirus group K member 24 Env polyprotein / Endogenous retrovirus group K member 25 Env polyprotein / Endogenous retrovirus group K member 6 Env polyprotein / Endogenous retrovirus group K member 8 Env polyprotein / Endogenous retrovirus group K member 9 Env polyprotein


分子量: 17162.525 Da / 分子数: 2 / 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 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q2N0S6

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抗体 , 4種, 8分子 LJEGFHIK

#3: 抗体 PGT122 Fab light chain


分子量: 22560.941 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 VRC34.01 Fab heavy chain


分子量: 23797.615 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 VRC34.01 Fab light chain


分子量: 23138.766 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#6: 抗体 PGT122 Fab heavy chain


分子量: 25434.691 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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糖 , 8種, 43分子

#7: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 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]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: 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
#9: 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: 14 / 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
#10: 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-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#11: 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: 4 / 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
#12: 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-(1-6)]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: 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[DManpa1-2DManpa1-3[DManpa1-6]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-j1_h2-i1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: 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: 1 / 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
#14: 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: 16 / 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: 5.17 Å3/Da / 溶媒含有率: 76.22 %
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: 0.5M Sodium Chloride, 0.1M Tris-HCl pH8.5, 5% PEG 8000 and 20% 2-methyl-2, 4- pentanediol

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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: 2015年3月15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: 4.3→50 Å / Num. obs: 39396 / % possible obs: 82.7 % / 冗長度: 4.6 % / Biso Wilson estimate: 127.24 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.063 / Rrim(I) all: 0.14 / Χ2: 0.766 / Net I/av σ(I): 9.812 / Net I/σ(I): 3.7 / Num. measured all: 182597
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
4.3-4.454.20.90323820.8240.4350.66350.7
4.45-4.634.30.80926540.8780.3860.69656.10.901
4.63-4.844.30.75631430.9210.3580.68666.80.84
4.84-5.14.40.59937730.9430.2840.67279.80.666
5.1-5.424.70.62542470.9460.2960.67689.80.694
5.42-5.834.90.50245400.9540.2370.68695.70.557
5.83-6.424.80.37346540.9690.1770.70497.90.415
6.42-7.354.80.21446690.9870.1010.75897.90.238
7.35-9.254.80.09346490.9960.0440.87296.60.104
9.25-504.60.05446850.9970.0261.09594.30.06

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
HKL-2000データ収集
HKL-2000データスケーリング
PDB_EXTRACT3.2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 / 解像度: 4.301→48.343 Å / SU ML: 0.71 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 43.87 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.309 1315 5.1 %
Rwork0.2811 24471 -
obs0.2825 25786 54.9 %
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
原子変位パラメータBiso max: 423.48 Å2 / Biso mean: 215.7774 Å2 / Biso min: 102.56 Å2
精密化ステップサイクル: final / 解像度: 4.301→48.343 Å
タンパク質核酸リガンド溶媒全体
原子数22452 0 1486 0 23938
Biso mean--231.65 --
残基数----2915
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00624611
X-RAY DIFFRACTIONf_angle_d1.19633715
X-RAY DIFFRACTIONf_chiral_restr0.0674125
X-RAY DIFFRACTIONf_plane_restr0.0054109
X-RAY DIFFRACTIONf_dihedral_angle_d12.814633
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4884X-RAY DIFFRACTION5.236TORSIONAL
12C4884X-RAY DIFFRACTION5.236TORSIONAL
21L1826X-RAY DIFFRACTION5.236TORSIONAL
22J1826X-RAY DIFFRACTION5.236TORSIONAL
31B1158X-RAY DIFFRACTION5.236TORSIONAL
32D1158X-RAY DIFFRACTION5.236TORSIONAL
41G4117X-RAY DIFFRACTION5.236TORSIONAL
42E4117X-RAY DIFFRACTION5.236TORSIONAL
51K2036X-RAY DIFFRACTION5.236TORSIONAL
52I2036X-RAY DIFFRACTION5.236TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.301-4.47310.3529130.35231641773
4.4731-4.67650.3542330.321847050310
4.6765-4.92290.3672450.32286591018
4.9229-5.23090.3006610.30251463152430
5.2309-5.63430.33191320.31852485261750
5.6343-6.20020.36022320.34334580481292
6.2002-7.0950.36132710.33374845511698
7.095-8.92970.31242730.28244819509297
8.9297-48.34610.26012550.22724780503593
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4590.8303-0.64921.22050.59711.5166-0.9617-0.50940.2383-0.12931.16640.71240.4316-0.67650.05391.3588-0.0213-0.01950.75610.08231.29429.176517.5424175.5241
21.98860.50260.82051.00791.20181.37860.0239-0.67080.19320.0593-0.5773-0.44540.07330.1648-0.00051.13980.0588-0.02050.92510.03371.438212.41216.9977209.8937
30.35771.0868-0.38261.45060.56521.35770.1117-1.3709-0.180.25050.26020.4027-1.44420.10780.0271.9478-0.1569-0.04750.4495-0.07251.23414.369530.931192.8374
40.44340.211-0.25440.3425-0.15750.229-0.21350.36150.1317-0.18490.10230.1478-0.1919-0.00840.35051.5706-1.0469-0.84520.9617-0.43772.079619.682922.183151.7039
50.20140.6226-0.08211.84520.07532.06440.8174-0.1771-1.1563-0.2710.2817-0.0456-0.8010.4160.46830.96470.5308-0.26570.6457-0.20381.47929.10819.0878154.2002
60.3606-0.14240.11870.8977-0.29350.1068-0.0978-0.10630.3057-0.21320.0974-0.3944-0.1409-0.0379-0.21671.7997-0.9459-0.05180.4333-1.01931.65796.9795.9893179.2107
75.0469-0.0136-1.05660.21790.0430.2384-0.30161.01070.32881.0370.11770.4646-0.171-0.232-0.3221.1898-0.56150.21250.3490.00571.3394-1.62986.7392164.5561
80.12590.41990.33161.39071.11790.9048-1.00230.2484-1.0473-0.71090.176-0.5795-0.35380.8613-0.67762.1617-0.52090.44741.43640.93491.8052-4.774612.7405146.543
90.0536-0.0410.04620.0324-0.02090.0613-0.48460.31580.29280.84280.04370.8298-0.2645-0.4233-0.00121.75270.4235-0.33151.3816-0.0012.7531-7.279629.9378145.5735
100.5256-0.7831-0.47321.15660.69680.41980.30050.00310.0853-0.3390.326-0.1039-0.2191-0.23661.59852.28821.5509-0.3021.29130.28921.6244-1.709328.0003153.491
110.5246-0.6687-0.21861.16210.83231.0984-0.1991-0.5107-0.73540.7042-0.03810.59270.3082-0.55210.04351.73290.82711.3062.96381.59872.1322-13.708215.596151.8569
121.1625-0.8954-1.00420.95750.95280.99520.6654-0.45370.1014-0.53081.0721-0.36450.2221-0.49990.29362.4432-0.5460.05411.91741.17382.7469-15.047-0.2212139.706
130.23130.63790.94760.21671.82282.5382-0.47480.06330.03230.07270.35110.1738-0.2578-0.32860.07491.64610.1331-0.07951.2434-0.16721.3752104.869172.2717258.3064
141.2789-0.21550.27040.1073-0.70742.6684-0.30850.3209-0.221-0.23370.1271-0.3635-0.73630.0372-0.00741.18960.4894-0.22990.989-0.24211.276191.587176.0849256.2911
150.0735-0.0296-0.0420.01480.00930.18660.83380.7351-0.36470.9138-1.0869-0.21120.9094-1.15202.70520.45060.04692.1688-0.23482.626485.451934.9837217.1914
160.2399-0.25840.13030.3273-0.23150.1444-0.41250.8733-0.55490.11971.4548-1.24150.6841-0.0410.00022.2026-0.52580.19842.2263-0.31691.716477.259341.7161219.8098
170.03850.29150.11351.08410.52050.33860.73861.0656-0.75610.40870.481-0.7579-0.26260.05860.02741.13380.3905-0.14092.6463-0.78872.277878.643431.3582194.4003
180.0182-0.07520.06680.1069-0.10150.0750.4490.5992-0.90120.6283-1.4112-1.46140.40610.1729-0.00871.5899-0.0959-0.04323.4851-1.05292.274177.831820.8333178.4362
191.0867-0.07230.25242.7595-0.51531.10980.37920.1454-0.07760.0980.88390.7445-0.19330.45221.09291.0741-2.1013-0.38560.9587-0.31670.840136.738528.3363154.76
200.5978-0.20560.14690.34060.08350.5579-0.38521.3617-0.10120.3765-0.1130.9638-1.77490.25770.11913.0189-1.2266-0.25021.5554-1.04171.280656.807951.6864173.1813
210.925-0.18390.03861.20710.20750.0544-0.29640.67530.3220.00880.2843-0.574-0.7059-0.02640.0633.5738-0.73720.15711.31120.10030.92931.983448.7384143.4935
221.7247-0.7752-0.5313.80340.550.2824-0.6026-0.13440.2349-1.64210.02361.5005-1.76990.3498-1.56092.5928-1.28620.1122.0870.35670.68736.223250.268153.4181
232.2361-0.468-2.60241.01560.87093.2008-0.90381.9829-0.3951-0.19380.9984-1.34281.6746-1.90330.0824.4183-1.8416-0.68152.74260.43022.392460.730760.9057159.1909
240.7723-0.05510.00173.91940.3040.15270.4981-0.357-0.8955-0.7325-0.2483-0.52830.2836-0.6556-0.24360.3161-0.0739-0.24382.5914-0.05661.393483.820754.35295.8594
250.36640.56710.15670.97830.4760.40060.5433-0.13590.0129-0.2103-1.11310.37390.1501-0.5542-0.00011.96350.0066-0.63262.53810.08331.87453.60148.0733277.5068
260.0661-0.0422-0.08840.04430.0780.15860.5468-0.1505-0.766-0.21540.60920.58010.3739-0.29292.17191.38621.332-1.16551.7997-0.06441.901497.379166.4418298.969
271.4437-0.00141.820.00220.0042.2883-0.2864-0.28460.34070.3186-0.4485-0.1548-0.2394-0.587-1.28090.72191.12390.08561.1801-0.25381.7224105.180174.3556296.6287
280.33070.47990.33690.90810.27010.5603-0.1241-0.84850.3012-0.00290.11110.6693-0.20610.2054-0.17760.67540.7186-0.03772.14940.15751.419117.373969.927271.3935
290.7645-0.58060.92140.6735-0.70791.2007-0.76750.83980.59160.8512-0.4979-0.3229-1.15810.2463-0.42321.2390.02680.62230.68810.00391.1345118.307782.298294.9184
300.1568-0.0533-0.15990.04350.0540.15780.27080.2433-0.20850.0008-0.08050.4905-0.0892-0.1640.32942.16680.1976-0.05612.0775-1.64373.2193100.361991.0886306.8661
310.6077-0.77230.76422.092-0.50731.14560.0806-1.21080.064-0.18051.6280.8972-0.9679-0.75830.15521.7570.2726-0.6042.4434-1.0122.127102.753288.1511297.3953
320.185-0.20570.00470.2428-0.0043-0.00410.12440.18670.153-0.39690.1476-0.614-0.25120.2222-0.06491.78190.13581.23370.5022-0.21261.9426119.367692.4677298.9632
330.90330.11940.49690.22630.08870.27740.2343-0.3023-0.41250.01020.44450.3911-0.1793-0.17830.82623.59020.08271.36090.97980.18582.1786133.945885.9461311.0011
340.25960.3020.23720.35580.28150.29280.4648-0.467-0.87010.1042-1.4372-0.13470.7021-1.6797-0.05441.70280.76470.0643.36660.02532.404662.698267.8026305.6541
352.90722.0048-0.90111.4019-0.61750.2744-0.2827-1.4848-0.4107-0.7364-0.6283-0.06520.2418-0.0053-0.71861.36660.68690.3412.3262-0.4320.500872.586168.4955308.763
360.1661-0.117-0.01580.09070.0079-0.00390.54860.84850.1285-0.3984-0.5125-0.26160.26950.363-0.57560.52770.7678-0.08572.3888-0.34691.346774.906372.6661297.3233
370.60730.0061-0.47280.7155-0.07731.0121-0.3504-0.1082-0.7415-0.8351-0.75310.7167-0.4797-0.2426-1.71721.64841.73410.19372.8653-0.56941.413270.667769.3938304.2881
380.0602-0.0292-0.06160.0491-0.01060.0873-0.512-0.316-0.42770.3705-0.4604-0.0397-0.31520.33640.00112.59170.5133-1.32153.7341-0.54162.558849.819668.0201294.3482
390.2851-0.0139-0.04260.2309-0.12510.0723-0.14660.2852-0.26721.09210.37790.16370.0545-1.7734-0.00142.0855-0.43510.25744.58730.32641.885244.823147.7158287.9251
400.9316-0.49740.00310.48640.30240.4226-0.0258-0.84460.63240.46010.3685-0.27410.1369-0.58460.68260.99660.977-0.32883.82770.96611.676249.141753.4417292.1957
410.385-0.20540.37410.2837-0.45910.73770.0856-1.0915-0.47450.722-0.8345-0.3305-0.40160.3377-0.321.2287-1.59270.03613.96620.09242.318339.483844.2544290.7866
420.5601-0.216-0.01590.26790.09880.0449-0.164-0.34030.37320.4022-1.0084-1.3518-1.3442-0.90440.00082.8051-0.6051-0.4042.0401-0.01932.039443.063540.0234245.9912
430.05870.0377-0.00660.06730.0660.11240.6106-0.6002-0.8220.46960.5185-0.14990.1295-0.8067-0.00071.9519-0.3189-0.49752.6868-0.39371.818135.592439.7931248.5024
440.17890.35460.48311.79720.50940.9296-0.3507-0.2473-0.4207-0.72090.09140.59381.6932-0.9644-0.13780.423-0.3859-0.81242.23570.37152.367749.700534.0954245.6412
450.17720.26490.2840.53420.22770.51822.7486-0.23120.2242.2068-2.5171-0.48451.03670.06640.00371.7926-0.4145-0.03133.3302-0.37972.763665.270734.2699263.3984
460.378-0.18690.12110.1032-0.06570.04310.06810.073-0.1385-0.6654-0.254-0.17630.2029-0.04210.00011.22020.0097-0.4952.7445-0.25472.02751.419422.6026232.5063
470.1635-0.26330.11940.404-0.24970.16771.4211-0.9681-0.37562.43680.5781-1.02580.2925-1.53560.03173.2714-0.4551-0.99423.13610.18972.644468.499717.6587267.2367
480.20190.43450.49560.99120.97011.2892-0.55250.7796-0.3173-0.0715-0.24690.1506-0.6063-0.5913-1.21980.7277-2.7704-0.58053.4579-1.2341.954570.658859.1217203.6285
490.8017-1.1699-0.28071.33570.61440.113-1.25740.6042-0.28380.31431.3680.5631-0.142.26720.10021.8532-0.57180.2512.4975-0.31481.815771.339347.9558204.7792
500.5556-0.23460.05260.1065-0.03370.00340.16572.07450.34231.04790.50571.1971-1.70210.98180.01123.2202-1.63510.01622.17240.51672.863363.455534.7103186.8987
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 117 )A31 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 235 )A118 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 507 )A236 - 507
4X-RAY DIFFRACTION4chain 'B' and (resid 512 through 523 )B512 - 523
5X-RAY DIFFRACTION5chain 'B' and (resid 524 through 544 )B524 - 544
6X-RAY DIFFRACTION6chain 'B' and (resid 545 through 575 )B545 - 575
7X-RAY DIFFRACTION7chain 'B' and (resid 576 through 595 )B576 - 595
8X-RAY DIFFRACTION8chain 'B' and (resid 596 through 610 )B596 - 610
9X-RAY DIFFRACTION9chain 'B' and (resid 611 through 622 )B611 - 622
10X-RAY DIFFRACTION10chain 'B' and (resid 623 through 637 )B623 - 637
11X-RAY DIFFRACTION11chain 'B' and (resid 638 through 650 )B638 - 650
12X-RAY DIFFRACTION12chain 'B' and (resid 651 through 664 )B651 - 664
13X-RAY DIFFRACTION13chain 'C' and (resid 31 through 258 )C31 - 258
14X-RAY DIFFRACTION14chain 'C' and (resid 259 through 505 )C259 - 505
15X-RAY DIFFRACTION15chain 'L' and (resid 6 through 26 )L6 - 26
16X-RAY DIFFRACTION16chain 'L' and (resid 27 through 89 )L27 - 89
17X-RAY DIFFRACTION17chain 'L' and (resid 90 through 174 )L90 - 174
18X-RAY DIFFRACTION18chain 'L' and (resid 175 through 210 )L175 - 210
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 111 )E1 - 111
20X-RAY DIFFRACTION20chain 'E' and (resid 112 through 214 )E112 - 214
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 38 )F1 - 38
22X-RAY DIFFRACTION22chain 'F' and (resid 39 through 128 )F39 - 128
23X-RAY DIFFRACTION23chain 'F' and (resid 129 through 212 )F129 - 212
24X-RAY DIFFRACTION24chain 'G' and (resid 1 through 111 )G1 - 111
25X-RAY DIFFRACTION25chain 'G' and (resid 112 through 214 )G112 - 214
26X-RAY DIFFRACTION26chain 'D' and (resid 512 through 523 )D512 - 523
27X-RAY DIFFRACTION27chain 'D' and (resid 524 through 544 )D524 - 544
28X-RAY DIFFRACTION28chain 'D' and (resid 545 through 575 )D545 - 575
29X-RAY DIFFRACTION29chain 'D' and (resid 576 through 615 )D576 - 615
30X-RAY DIFFRACTION30chain 'D' and (resid 616 through 622 )D616 - 622
31X-RAY DIFFRACTION31chain 'D' and (resid 623 through 637 )D623 - 637
32X-RAY DIFFRACTION32chain 'D' and (resid 638 through 650 )D638 - 650
33X-RAY DIFFRACTION33chain 'D' and (resid 651 through 664 )D651 - 664
34X-RAY DIFFRACTION34chain 'H' and (resid 1 through 18 )H1 - 18
35X-RAY DIFFRACTION35chain 'H' and (resid 19 through 38 )H19 - 38
36X-RAY DIFFRACTION36chain 'H' and (resid 39 through 61 )H39 - 61
37X-RAY DIFFRACTION37chain 'H' and (resid 62 through 102 )H62 - 102
38X-RAY DIFFRACTION38chain 'H' and (resid 103 through 113 )H103 - 113
39X-RAY DIFFRACTION39chain 'H' and (resid 114 through 150 )H114 - 150
40X-RAY DIFFRACTION40chain 'H' and (resid 151 through 174 )H151 - 174
41X-RAY DIFFRACTION41chain 'H' and (resid 175 through 212 )H175 - 212
42X-RAY DIFFRACTION42chain 'I' and (resid 1 through 56 )I1 - 56
43X-RAY DIFFRACTION43chain 'I' and (resid 57 through 87 )I57 - 87
44X-RAY DIFFRACTION44chain 'I' and (resid 88 through 141 )I88 - 141
45X-RAY DIFFRACTION45chain 'I' and (resid 142 through 211 )I142 - 211
46X-RAY DIFFRACTION46chain 'J' and (resid 6 through 114 )J6 - 114
47X-RAY DIFFRACTION47chain 'J' and (resid 115 through 210 )J115 - 210
48X-RAY DIFFRACTION48chain 'K' and (resid 1 through 87 )K1 - 87
49X-RAY DIFFRACTION49chain 'K' and (resid 88 through 141 )K88 - 141
50X-RAY DIFFRACTION50chain 'K' and (resid 142 through 211 )K142 - 211

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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

他の情報も見る