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- PDB-4hg4: Crystal structure of Fab 2G1 in complex with a H2N2 influenza vir... -

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基本情報

登録情報
データベース: PDB / ID: 4hg4
タイトルCrystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin
要素
  • (Hemagglutinin ...) x 2
  • Fab 2G1 heavy chain
  • Fab 2G1 light chain
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / 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 Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Hemagglutinin / Hemagglutinin
類似検索 - 構成要素
生物種Influenza A virus (A型インフルエンザウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Xu, R. / Wilson, I.A.
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2013
タイトル: A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.
著者: Xu, R. / Krause, J.C. / McBride, R. / Paulson, J.C. / Crowe, J.E. / Wilson, I.A.
履歴
登録2012年10月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年2月13日Provider: repository / タイプ: Initial release
改定 1.12013年5月22日Group: Database references
改定 1.22017年11月15日Group: Refinement description / カテゴリ: software / Item: _software.classification / _software.name
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年11月6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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Hemagglutinin HA1
a: Hemagglutinin HA2
B: Hemagglutinin HA1
b: Hemagglutinin HA2
C: Hemagglutinin HA1
c: Hemagglutinin HA2
D: Hemagglutinin HA1
d: Hemagglutinin HA2
E: Hemagglutinin HA1
e: Hemagglutinin HA2
F: Hemagglutinin HA1
f: Hemagglutinin HA2
G: Hemagglutinin HA1
g: Hemagglutinin HA2
H: Hemagglutinin HA1
h: Hemagglutinin HA2
I: Hemagglutinin HA1
i: Hemagglutinin HA2
J: Fab 2G1 heavy chain
K: Fab 2G1 light chain
L: Fab 2G1 heavy chain
M: Fab 2G1 light chain
N: Fab 2G1 heavy chain
O: Fab 2G1 light chain
P: Fab 2G1 heavy chain
Q: Fab 2G1 light chain
R: Fab 2G1 heavy chain
S: Fab 2G1 light chain
T: Fab 2G1 heavy chain
U: Fab 2G1 light chain
V: Fab 2G1 heavy chain
W: Fab 2G1 light chain
X: Fab 2G1 heavy chain
Y: Fab 2G1 light chain
Z: Fab 2G1 heavy chain
z: Fab 2G1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)939,77251
ポリマ－933,89436
非ポリマー5,87815
水00
1
A: Hemagglutinin HA1
a: Hemagglutinin HA2
B: Hemagglutinin HA1
b: Hemagglutinin HA2
C: Hemagglutinin HA1
c: Hemagglutinin HA2
J: Fab 2G1 heavy chain
K: Fab 2G1 light chain
L: Fab 2G1 heavy chain
M: Fab 2G1 light chain
N: Fab 2G1 heavy chain
O: Fab 2G1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)313,17617
ポリマ－311,29812
非ポリマー1,8785
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Hemagglutinin HA1
d: Hemagglutinin HA2
E: Hemagglutinin HA1
e: Hemagglutinin HA2
F: Hemagglutinin HA1
f: Hemagglutinin HA2
P: Fab 2G1 heavy chain
Q: Fab 2G1 light chain
R: Fab 2G1 heavy chain
S: Fab 2G1 light chain
T: Fab 2G1 heavy chain
U: Fab 2G1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)313,01417
ポリマ－311,29812
非ポリマー1,7165
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: Hemagglutinin HA1
g: Hemagglutinin HA2
H: Hemagglutinin HA1
h: Hemagglutinin HA2
I: Hemagglutinin HA1
i: Hemagglutinin HA2
V: Fab 2G1 heavy chain
W: Fab 2G1 light chain
X: Fab 2G1 heavy chain
Y: Fab 2G1 light chain
Z: Fab 2G1 heavy chain
z: Fab 2G1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)313,58217
ポリマ－311,29812
非ポリマー2,2845
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)126.842, 133.143, 812.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain F and (resseq 20:53 or resseq 53:81 or resseq...
21chain G and (resseq 20:53 or resseq 53:81 or resseq...
31chain H and (resseq 20:53 or resseq 53:81 or resseq...
41chain I and (resseq 20:53 or resseq 53:81 or resseq...
12chain C and (resseq 10:53 or resseq 53:81 or resseq...
22chain D and (resseq 10:53 or resseq 53:81 or resseq...
32chain E and (resseq 10:53 or resseq 53:81 or resseq...
13chain A and (resseq 13:53 or resseq 53:81 or resseq...
23chain B and (resseq 13:53 or resseq 53:81 or resseq...
14chain c and (resseq 1:60 or resseq 66:172 )
24chain d and (resseq 1:60 or resseq 66:172 )
34chain e and (resseq 1:60 or resseq 66:172 )
44chain f and (resseq 1:60 or resseq 66:172 )
54chain g and (resseq 1:60 or resseq 66:172 )
64chain h and (resseq 1:60 or resseq 66:172 )
74chain i and (resseq 1:60 or resseq 66:172 )
15chain a and (resseq 1:60 or resseq 66:138 or resseq 144:171 )
25chain b and (resseq 1:60 or resseq 66:138 or resseq 144:171 )
16chain X and (resseq 2:52 or resseq 52:82 or resseq...
26chain Z and (resseq 2:52 or resseq 52:82 or resseq...
17chain V and (resseq 2:52 or resseq 52:82 or resseq...
27chain P and (resseq 2:52 or resseq 52:82 or resseq...
37chain R and (resseq 2:52 or resseq 52:82 or resseq...
47chain T and (resseq 2:52 or resseq 52:82 or resseq...
18chain z and (resseq 1:104 or resseq 156:165 or resseq 175:179 )
28chain Q and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )
38chain S and (resseq 1:153 or resseq 155:211 )
48chain U and (resseq 1:153 or resseq 155:211 )
58chain W and (resseq 1:105 )
68chain Y and (resseq 1:109 )
19chain M and (resseq 1:212 )
29chain O and (resseq 1:212 )
110chain L and (resseq 1:127 or resseq 136:213 )
210chain N and (resseq 1:127 or resseq 136:213 )

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYSchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK20 - 5312 - 45
121LYSLYSSERSERchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK53 - 8145 - 74
131SERSERASPASPchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK81 - 9574 - 89
141ASPASPLYSLYSchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK95 - 11689 - 111
151LYSLYSLYSLYSchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK116111
161LYSLYSLYSLYSchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK116111
171LYSLYSLYSLYSchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK116 - 123111 - 121
181ASPASPARGARGchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK125 - 263122 - 260
191ARGARGILEILEchain 'F' and (resseq 20:53 or resseq 53:81 or resseq...FK263 - 326260 - 324
211ASNASNLYSLYSchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM20 - 5312 - 45
221LYSLYSSERSERchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM53 - 8145 - 74
231SERSERASPASPchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM81 - 9574 - 89
241ASPASPLYSLYSchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM95 - 11689 - 111
251LYSLYSLYSLYSchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM116111
261LYSLYSLYSLYSchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM116111
271LYSLYSLYSLYSchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM116 - 123111 - 121
281ASPASPARGARGchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM125 - 263122 - 260
291ARGARGILEILEchain 'G' and (resseq 20:53 or resseq 53:81 or resseq...GM263 - 326260 - 324
311ASNASNLYSLYSchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO20 - 5312 - 45
321LYSLYSSERSERchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO53 - 8145 - 74
331SERSERASPASPchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO81 - 9574 - 89
341ASPASPLYSLYSchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO95 - 11689 - 111
351LYSLYSLYSLYSchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO116111
361LYSLYSLYSLYSchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO116111
371LYSLYSLYSLYSchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO116 - 123111 - 121
381ASPASPARGARGchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO125 - 263122 - 260
391ARGARGILEILEchain 'H' and (resseq 20:53 or resseq 53:81 or resseq...HO263 - 326260 - 324
411ASNASNLYSLYSchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ20 - 5312 - 45
421LYSLYSSERSERchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ53 - 8145 - 74
431SERSERASPASPchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ81 - 9574 - 89
441ASPASPLYSLYSchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ95 - 11689 - 111
451LYSLYSLYSLYSchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ116111
461LYSLYSLYSLYSchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ116111
471LYSLYSLYSLYSchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ116 - 123111 - 121
481ASPASPARGARGchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ125 - 263122 - 260
491ARGARGILEILEchain 'I' and (resseq 20:53 or resseq 53:81 or resseq...IQ263 - 326260 - 324
112GLYGLYLYSLYSchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE10 - 532 - 45
122LYSLYSSERSERchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE53 - 8145 - 74
132SERSERASPASPchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE81 - 9574 - 89
142ASPASPLYSLYSchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE95 - 11689 - 111
152LYSLYSLYSLYSchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE116111
162LYSLYSLYSLYSchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE116111
172LYSLYSLYSLYSchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE116 - 123111 - 121
182ASPASPARGARGchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE125 - 263122 - 260
192ARGARGILEILEchain 'C' and (resseq 10:53 or resseq 53:81 or resseq...CE263 - 326260 - 324
212GLYGLYLYSLYSchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG10 - 532 - 45
222LYSLYSSERSERchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG53 - 8145 - 74
232SERSERASPASPchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG81 - 9574 - 89
242ASPASPLYSLYSchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG95 - 11689 - 111
252LYSLYSLYSLYSchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG116111
262LYSLYSLYSLYSchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG116111
272LYSLYSLYSLYSchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG116 - 123111 - 121
282ASPASPARGARGchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG125 - 263122 - 260
292ARGARGILEILEchain 'D' and (resseq 10:53 or resseq 53:81 or resseq...DG263 - 326260 - 324
312GLYGLYLYSLYSchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI10 - 532 - 45
322LYSLYSSERSERchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI53 - 8145 - 74
332SERSERASPASPchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI81 - 9574 - 89
342ASPASPLYSLYSchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI95 - 11689 - 111
352LYSLYSLYSLYSchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI116111
362LYSLYSLYSLYSchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI116111
372LYSLYSLYSLYSchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI116 - 123111 - 121
382ASPASPARGARGchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI125 - 263122 - 260
392ARGARGGLNGLNchain 'E' and (resseq 10:53 or resseq 53:81 or resseq...EI263 - 325260 - 323
113ILEILELYSLYSchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA13 - 535 - 45
123LYSLYSSERSERchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA53 - 8145 - 74
133SERSERASPASPchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA81 - 9574 - 89
143ASPASPLYSLYSchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA95 - 11689 - 111
153LYSLYSLYSLYSchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA116111
163LYSLYSLYSLYSchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA116111
173LYSLYSLYSLYSchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA116 - 123111 - 121
183ASPASPARGARGchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA125 - 263122 - 260
193ARGARGGLNGLNchain 'A' and (resseq 13:53 or resseq 53:81 or resseq...AA263 - 325260 - 323
213ILEILELYSLYSchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC13 - 535 - 45
223LYSLYSSERSERchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC53 - 8145 - 74
233SERSERASPASPchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC81 - 9574 - 89
243ASPASPLYSLYSchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC95 - 11689 - 111
253LYSLYSLYSLYSchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC116111
263LYSLYSLYSLYSchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC116111
273LYSLYSLYSLYSchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC116 - 123111 - 121
283ASPASPARGARGchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC125 - 263122 - 260
293ARGARGGLNGLNchain 'B' and (resseq 13:53 or resseq 53:81 or resseq...BC263 - 325260 - 323
114GLYGLYASNASNchain 'c' and (resseq 1:60 or resseq 66:172 )cF1 - 601 - 60
124VALVALGLUGLUchain 'c' and (resseq 1:60 or resseq 66:172 )cF66 - 17266 - 172
214GLYGLYASNASNchain 'd' and (resseq 1:60 or resseq 66:172 )dH1 - 601 - 60
224VALVALGLUGLUchain 'd' and (resseq 1:60 or resseq 66:172 )dH66 - 17266 - 172
314GLYGLYASNASNchain 'e' and (resseq 1:60 or resseq 66:172 )eJ1 - 601 - 60
324VALVALGLUGLUchain 'e' and (resseq 1:60 or resseq 66:172 )eJ66 - 17266 - 172
414GLYGLYASNASNchain 'f' and (resseq 1:60 or resseq 66:172 )fL1 - 601 - 60
424VALVALGLUGLUchain 'f' and (resseq 1:60 or resseq 66:172 )fL66 - 17266 - 172
514GLYGLYASNASNchain 'g' and (resseq 1:60 or resseq 66:172 )gN1 - 601 - 60
524VALVALGLUGLUchain 'g' and (resseq 1:60 or resseq 66:172 )gN66 - 17266 - 172
614GLYGLYASNASNchain 'h' and (resseq 1:60 or resseq 66:172 )hP1 - 601 - 60
624VALVALGLUGLUchain 'h' and (resseq 1:60 or resseq 66:172 )hP66 - 17266 - 172
714GLYGLYASNASNchain 'i' and (resseq 1:60 or resseq 66:172 )iR1 - 601 - 60
724VALVALGLUGLUchain 'i' and (resseq 1:60 or resseq 66:172 )iR66 - 17266 - 172
115GLYGLYASNASNchain 'a' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )aB1 - 601 - 60
125VALVALPHEPHEchain 'a' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )aB66 - 13866 - 138
135CYSCYSASNASNchain 'a' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )aB144 - 171144 - 171
215GLYGLYASNASNchain 'b' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )bD1 - 601 - 60
225VALVALPHEPHEchain 'b' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )bD66 - 13866 - 138
235CYSCYSASNASNchain 'b' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )bD144 - 171144 - 171
116VALVALILEILEchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA2 - 522 - 52
126ILEILELEULEUchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA52 - 8252 - 83
136LEULEULEULEUchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA8283
146LEULEULEULEUchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA8283
156LEULEUTYRTYRchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA82 - 10083 - 104
166TYRTYRTYRTYRchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA100104
176TYRTYRTYRTYRchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA100104
186TYRTYRSERSERchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA100 - 120104 - 127
196LEULEUVALVALchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA141 - 150148 - 157
1106THRTHRSERSERchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA165 - 179172 - 186
1116ASNASNTHRTHRchain 'X' and (resseq 2:52 or resseq 52:82 or resseq...XGA197 - 205204 - 212
216VALVALILEILEchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA2 - 522 - 52
226ILEILELEULEUchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA52 - 8252 - 83
236LEULEULEULEUchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA8283
246LEULEULEULEUchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA8283
256LEULEUTYRTYRchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA82 - 10083 - 104
266TYRTYRTYRTYRchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA100104
276TYRTYRTYRTYRchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA100104
286TYRTYRSERSERchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA100 - 120104 - 127
296LEULEUVALVALchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA141 - 150148 - 157
2106THRTHRSERSERchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA165 - 179172 - 186
2116ASNASNTHRTHRchain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...ZIA197 - 205204 - 212
117VALVALILEILEchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA2 - 522 - 52
127ILEILELEULEUchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA52 - 8252 - 83
137LEULEULEULEUchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA8283
147LEULEULEULEUchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA8283
157LEULEUTYRTYRchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA82 - 10083 - 104
167TYRTYRTYRTYRchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA100104
177TYRTYRTYRTYRchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA100104
187TYRTYRVALVALchain 'V' and (resseq 2:52 or resseq 52:82 or resseq...VEA100 - 111104 - 118
217VALVALILEILEchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY2 - 522 - 52
227ILEILELEULEUchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY52 - 8252 - 83
237LEULEULEULEUchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY8283
247LEULEULEULEUchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY8283
257LEULEUTYRTYRchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY82 - 10083 - 104
267TYRTYRTYRTYRchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY100104
277TYRTYRTYRTYRchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY100104
287TYRTYRPROPROchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY100 - 119104 - 126
297VALVALGLUGLUchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY142 - 148149 - 155
2107TRPTRPVALVALchain 'P' and (resseq 2:52 or resseq 52:82 or resseq...PY154 - 181161 - 188
317VALVALILEILEchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA2 - 522 - 52
327ILEILELEULEUchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA52 - 8252 - 83
337LEULEULEULEUchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA8283
347LEULEULEULEUchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA8283
357LEULEUTYRTYRchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA82 - 10083 - 104
367TYRTYRTYRTYRchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA100104
377TYRTYRTYRTYRchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA100104
387TYRTYRPROPROchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA100 - 126104 - 133
397ALAALAVALVALchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA137 - 184144 - 191
3107SERSERPROPROchain 'R' and (resseq 2:52 or resseq 52:82 or resseq...RAA188 - 213195 - 220
417VALVALILEILEchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA2 - 522 - 52
427ILEILELEULEUchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA52 - 8252 - 83
437LEULEULEULEUchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA8283
447LEULEULEULEUchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA8283
457LEULEUTYRTYRchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA82 - 10083 - 104
467TYRTYRTYRTYRchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA100104
477TYRTYRTYRTYRchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA100104
487TYRTYRPROPROchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA100 - 126104 - 133
497ALAALAVALVALchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA137 - 184144 - 191
4107SERSERPROPROchain 'T' and (resseq 2:52 or resseq 52:82 or resseq...TCA188 - 213195 - 220
118ASPASPLEULEUchain 'z' and (resseq 1:104 or resseq 156:165 or resseq 175:179 )zJA1 - 1041 - 104
128SERSERGLUGLUchain 'z' and (resseq 1:104 or resseq 156:165 or resseq 175:179 )zJA156 - 165156 - 165
138LEULEULEULEUchain 'z' and (resseq 1:104 or resseq 156:165 or resseq 175:179 )zJA175 - 179175 - 179
218ASPASPPHEPHEchain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )QZ1 - 1161 - 116
228VALVALALAALAchain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )QZ132 - 144132 - 144
238GLNGLNTHRTHRchain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )QZ160 - 178160 - 178
248VALVALPROPROchain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )QZ196 - 204196 - 204
318ASPASPALAALAchain 'S' and (resseq 1:153 or resseq 155:211 )SBA1 - 1531 - 153
328GLNGLNARGARGchain 'S' and (resseq 1:153 or resseq 155:211 )SBA155 - 211155 - 211
418ASPASPALAALAchain 'U' and (resseq 1:153 or resseq 155:211 )UDA1 - 1531 - 153
428GLNGLNARGARGchain 'U' and (resseq 1:153 or resseq 155:211 )UDA155 - 211155 - 211
518ASPASPGLUGLUchain 'W' and (resseq 1:105 )WFA1 - 1051 - 105
618ASPASPTHRTHRchain 'Y' and (resseq 1:109 )YHA1 - 1091 - 109
119ASPASPGLYGLYchain 'M' and (resseq 1:212 )MV1 - 2121 - 212
219ASPASPGLYGLYchain 'O' and (resseq 1:212 )OX1 - 2121 - 212
1110GLUGLUSERSERchain 'L' and (resseq 1:127 or resseq 136:213 )LU1 - 1271 - 134
1210ALAALAPROPROchain 'L' and (resseq 1:127 or resseq 136:213 )LU136 - 213143 - 220
2110GLUGLUSERSERchain 'N' and (resseq 1:127 or resseq 136:213 )NW1 - 1271 - 134
2210ALAALAPROPROchain 'N' and (resseq 1:127 or resseq 136:213 )NW136 - 213143 - 220

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixベクター
1given(-0.685079, -0.708405, -0.169792), (-0.636123, 0.468175, 0.613319), (-0.354986, 0.528181, -0.771369)-83.4879, 71.164703, -105.677002
2given(0.882724, -0.0446, -0.46777), (-0.009101, -0.996921, 0.077879), (-0.469803, -0.064489, -0.880412)-98.588402, -8.03648, -127.136002
3given(-0.41806, 0.902517, 0.103387), (0.904416, 0.402839, 0.140544), (0.085195, 0.152261, -0.984662)-27.149099, 24.132601, -132.906998
4given(-0.87393, 0.225282, 0.43069), (-0.414235, -0.808767, -0.417499), (0.254273, -0.543272, 0.800126)-108.667, 3.50978, -124.552002
5given(0.798859, 0.556833, 0.227511), (-0.584303, 0.808189, 0.073623), (-0.142876, -0.19175, 0.970988)-28.027599, 9.10435, -140.044998
6given(-0.408498, -0.912223, 0.031266), (0.76146, -0.359474, -0.539404), (0.503297, -0.196538, 0.841466)-68.831902, 22.6838, 20.3692
7given(-0.884297, 0.202418, 0.420768), (-0.391423, -0.81268, -0.431671), (0.254571, -0.546423, 0.797881)-109.956001, 4.30507, -124.657997
8given(0.786228, 0.573162, 0.230936), (-0.597413, 0.800555, 0.047005), (-0.157935, -0.17492, 0.971833)-29.214899, 8.20693, -140.514008
9given(0.214629, -0.971708, -0.098579), (0.904665, 0.235826, -0.354919), (0.368125, -0.013005, 0.929685)-68.733597, 73.118301, -114.931999
10given(0.484245, -0.712645, -0.507586), (-0.66758, -0.675948, 0.312141), (-0.565548, 0.187701, -0.803071)-140.856995, 57.519199, -246.906998
11given(0.316778, 0.944854, -0.083079), (0.944686, -0.322138, -0.061607), (-0.084972, -0.058967, -0.994637)-69.362801, 29.304001, -269.437012
12given(-0.993116, -0.109597, 0.041331), (-0.076378, 0.873455, 0.480876), (-0.088803, 0.47441, -0.875814)-78.020401, 102.115997, -248.311005
13given(-0.432813, -0.900289, 0.046387), (0.748172, -0.387436, -0.538639), (0.502903, -0.198425, 0.841259)-68.783401, 22.3314, 20.422701
14given(-0.428318, 0.700086, 0.571334), (-0.865807, -0.498957, -0.03768), (0.258692, -0.510804, 0.819852)66.806702, -32.628601, -27.302799
15given(-0.239992, 0.970602, -0.018331), (0.959981, 0.240089, 0.144202), (0.144364, 0.01701, -0.989378)-17.6532, 36.041698, -130.356995
16given(0.81577, -0.205191, -0.540755), (-0.240582, -0.970614, 0.005366), (-0.525965, 0.125719, -0.841163)21.4251, -30.923401, -161.098007
17given(-0.699382, -0.631457, -0.334853), (-0.685957, 0.461362, 0.56268), (-0.20082, 0.623223, -0.75582)-48.256199, -33.488499, -139.414993
18given(0.88285, -0.052921, -0.466664), (-0.093561, -0.993533, -0.064332), (-0.460242, 0.100457, -0.882092)26.3806, -23.048401, -156.785004
19given(-0.709319, -0.613053, -0.347896), (-0.695726, 0.529578, 0.485296), (-0.113275, 0.58627, -0.802157)-53.5229, -37.121201, -136.470993
20given(-0.490914, 0.869646, 0.052145), (0.868769, 0.484187, 0.103935), (0.065138, 0.096326, -0.993216)-26.819401, 28.2796, -132.563995
21given(-0.208026, 0.761349, 0.614063), (-0.956108, -0.290726, 0.036557), (0.206356, -0.579506, 0.78841)73.033997, -20.9161, -30.422501
22given(-0.406992, -0.885792, 0.223003), (0.708037, -0.460173, -0.535653), (0.577097, -0.060112, 0.81446)3.04171, -77.212303, -18.746799
23given(-0.450548, -0.890759, 0.059625), (0.75315, -0.415106, -0.510345), (0.479345, -0.185028, 0.8579)-70.828201, 29.440001, 21.8832
24given(-0.42756, -0.9023, 0.055197), (0.78096, -0.399435, -0.48016), (0.455296, -0.162191, 0.875442)-67.821701, 37.194901, 20.927999

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要素

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Hemagglutinin ... , 2種, 18分子 ABCDEFGHIabcdefghi

#1: タンパク質
Hemagglutinin HA1


分子量: 36573.379 Da / 分子数: 9 / 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/Japan/305+/1957(H2N2) / 遺伝子: HA / プラスミド: pFastBac / 細胞株 (発現宿主): Hi5 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q67085, UniProt: P03451*PLUS
#2: タンパク質
Hemagglutinin HA2


分子量: 20139.295 Da / 分子数: 9 / 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/Japan/305+/1957(H2N2) / 遺伝子: HA / プラスミド: pFastBac / 細胞株 (発現宿主): Hi5 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q67085, UniProt: P03451*PLUS

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抗体 , 2種, 18分子 JLNPRTVXZKMOQSUWYz

#3: 抗体
Fab 2G1 heavy chain


分子量: 23424.170 Da / 分子数: 9 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pEE6.4 / 細胞株 (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト)
#4: 抗体
Fab 2G1 light chain


分子量: 23629.189 Da / 分子数: 9 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pEE12.4 / 細胞株 (発現宿主): HEK 293F / 発現宿主: Homo sapiens (ヒト)

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糖 , 3種, 15分子

#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: 9 / 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
#6: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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: 4 / 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

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.67 Å3/Da / 溶媒含有率: 66.5 %
結晶化温度: 295.7 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 10% PEG6000, 0.1 M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 295.7K

-
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: SSRL / ビームライン: BL12-2 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年1月11日
詳細: Shutterless data collection; Fine phi slicing experiments
放射モノクロメーター: Liquid nitrogen-cooled double crystal
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: 0.9795 Å / 相対比: 1
Reflection冗長度: 6.6 % / Av σ(I) over netI: 11.53 / 数: 1549028 / Rmerge(I) obs: 0.133 / Χ2: 1.01 / D res high: 3.15 Å / D res low: 50 Å / Num. obs: 234983 / % possible obs: 98.7
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785098.510.070.9616.6
5.386.7898.910.0890.9326.7
4.75.3899.810.11.0166.9
4.274.798.310.1141.0166.6
3.974.2799.810.1610.9986.9
3.733.9799.710.2471.0827
3.553.7397.710.3261.0926.5
3.393.5599.610.4711.016.7
3.263.3999.510.6450.946.4
3.153.2695.610.8191.0755.5
反射解像度: 3.15→50 Å / Num. obs: 234983 / % possible obs: 98.7 % / 冗長度: 6.6 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.3
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsDiffraction-ID% possible all
3.15-3.265.50.819195.6
3.26-3.396.40.645199.5
3.39-3.556.70.471199.6
3.55-3.736.50.326197.7
3.73-3.9770.247199.7
3.97-4.276.90.161199.8
4.27-4.76.60.114198.3
4.7-5.386.90.1199.8
5.38-6.786.70.089198.9
6.78-506.60.07198.5

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIX1.7.2_869精密化
PDB_EXTRACT3.11データ抽出
Blu-Iceデータ収集
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.2→48.13 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.99 / σ(F): 0 / 位相誤差: 30.6 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3019 10333 5.02 %
Rwork0.249 --
obs0.2517 205778 90.25 %
溶媒の処理減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 23.003 Å2 / ksol: 0.286 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--4.7199 Å2-0 Å2-0 Å2
2---3.6156 Å20 Å2
3----7.4957 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→48.13 Å
タンパク質核酸リガンド溶媒全体
原子数58356 0 386 0 58742
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0160150
X-RAY DIFFRACTIONf_angle_d1.36681619
X-RAY DIFFRACTIONf_dihedral_angle_d20.83822062
X-RAY DIFFRACTIONf_chiral_restr0.0888963
X-RAY DIFFRACTIONf_plane_restr0.00710484
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11F2458X-RAY DIFFRACTIONPOSITIONAL0.035
12G2458X-RAY DIFFRACTIONPOSITIONAL0.035
13H2458X-RAY DIFFRACTIONPOSITIONAL0.036
14I2458X-RAY DIFFRACTIONPOSITIONAL0.023
21C2532X-RAY DIFFRACTIONPOSITIONAL0.041
22D2532X-RAY DIFFRACTIONPOSITIONAL0.041
23E2524X-RAY DIFFRACTIONPOSITIONAL0.05
31A2503X-RAY DIFFRACTIONPOSITIONAL0.036
32B2503X-RAY DIFFRACTIONPOSITIONAL0.036
41c1355X-RAY DIFFRACTIONPOSITIONAL0.029
42d1355X-RAY DIFFRACTIONPOSITIONAL0.029
43e1355X-RAY DIFFRACTIONPOSITIONAL0.033
44f1355X-RAY DIFFRACTIONPOSITIONAL0.041
45g1355X-RAY DIFFRACTIONPOSITIONAL0.029
46h1355X-RAY DIFFRACTIONPOSITIONAL0.03
47i1355X-RAY DIFFRACTIONPOSITIONAL0.033
51a1295X-RAY DIFFRACTIONPOSITIONAL0.032
52b1295X-RAY DIFFRACTIONPOSITIONAL0.032
61X1204X-RAY DIFFRACTIONPOSITIONAL0.024
62Z1204X-RAY DIFFRACTIONPOSITIONAL0.024
71V883X-RAY DIFFRACTIONPOSITIONAL0.028
72P883X-RAY DIFFRACTIONPOSITIONAL0.028
73R883X-RAY DIFFRACTIONPOSITIONAL0.02
74T883X-RAY DIFFRACTIONPOSITIONAL0.018
81z883X-RAY DIFFRACTIONPOSITIONAL0.037
82Q883X-RAY DIFFRACTIONPOSITIONAL0.037
83S915X-RAY DIFFRACTIONPOSITIONAL0.04
84U915X-RAY DIFFRACTIONPOSITIONAL0.036
85W809X-RAY DIFFRACTIONPOSITIONAL0.033
86Y809X-RAY DIFFRACTIONPOSITIONAL0.023
91M1646X-RAY DIFFRACTIONPOSITIONAL0.051
92O1646X-RAY DIFFRACTIONPOSITIONAL0.051
101L1578X-RAY DIFFRACTIONPOSITIONAL0.05
102N1578X-RAY DIFFRACTIONPOSITIONAL0.05
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.3956570.36151077X-RAY DIFFRACTION15
3.2364-3.27440.4125980.35211915X-RAY DIFFRACTION27
3.2744-3.31440.38351380.3332975X-RAY DIFFRACTION42
3.3144-3.35630.38232320.33134554X-RAY DIFFRACTION64
3.3563-3.40040.40543030.32626048X-RAY DIFFRACTION84
3.4004-3.4470.37473680.32486962X-RAY DIFFRACTION98
3.447-3.49620.34043800.31587122X-RAY DIFFRACTION100
3.4962-3.54840.35133830.31177116X-RAY DIFFRACTION100
3.5484-3.60380.373580.29867203X-RAY DIFFRACTION100
3.6038-3.66290.36953900.29257032X-RAY DIFFRACTION100
3.6629-3.72610.34113330.27966831X-RAY DIFFRACTION95
3.7261-3.79380.34493650.2747024X-RAY DIFFRACTION99
3.7938-3.86670.32563920.26857143X-RAY DIFFRACTION100
3.8667-3.94560.32443750.27127161X-RAY DIFFRACTION100
3.9456-4.03140.32044020.23447155X-RAY DIFFRACTION100
4.0314-4.12510.28433470.23627165X-RAY DIFFRACTION100
4.1251-4.22820.26773890.22687204X-RAY DIFFRACTION100
4.2282-4.34240.26384200.21937130X-RAY DIFFRACTION100
4.3424-4.47010.25113860.20677177X-RAY DIFFRACTION100
4.4701-4.61430.2613720.20956884X-RAY DIFFRACTION96
4.6143-4.77910.28713790.20537147X-RAY DIFFRACTION99
4.7791-4.97020.254300.2017194X-RAY DIFFRACTION100
4.9702-5.19620.26213660.20477202X-RAY DIFFRACTION100
5.1962-5.46980.24883890.22117235X-RAY DIFFRACTION100
5.4698-5.8120.2973790.23867293X-RAY DIFFRACTION100
5.812-6.25980.32923490.24427042X-RAY DIFFRACTION97
6.2598-6.88810.28963950.23237295X-RAY DIFFRACTION100
6.8881-7.88110.27413810.21577397X-RAY DIFFRACTION100
7.8811-9.91510.24723810.20267252X-RAY DIFFRACTION98
9.9151-48.13530.32323960.28847510X-RAY DIFFRACTION97
精密化 TLS手法: refined / Origin x: -48.7637 Å / Origin y: 13.0626 Å / Origin z: -109.0588 Å
111213212223313233
T0.1315 Å20.1082 Å2-0.0705 Å2-0.1323 Å20.0842 Å2--0.035 Å2
L-0.0944 °2-0.0695 °20.1271 °2--0.166 °2-0.2166 °2---0.0462 °2
S0.0458 Å °-0.2421 Å °-0.0413 Å °0.2168 Å °0.0394 Å °-0.0279 Å °0.0945 Å °0.0751 Å °0.0829 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 325
2X-RAY DIFFRACTION1alla1 - 171
3X-RAY DIFFRACTION1allB13 - 325
4X-RAY DIFFRACTION1allb1 - 172
5X-RAY DIFFRACTION1allC9 - 326
6X-RAY DIFFRACTION1allc1 - 172
7X-RAY DIFFRACTION1allD9 - 326
8X-RAY DIFFRACTION1alld1 - 172
9X-RAY DIFFRACTION1allE8 - 325
10X-RAY DIFFRACTION1alle1 - 172
11X-RAY DIFFRACTION1allF9 - 326
12X-RAY DIFFRACTION1allf1 - 172
13X-RAY DIFFRACTION1allG9 - 326
14X-RAY DIFFRACTION1allg1 - 172
15X-RAY DIFFRACTION1allH9 - 327
16X-RAY DIFFRACTION1allh1 - 172
17X-RAY DIFFRACTION1allI9 - 326
18X-RAY DIFFRACTION1alli1 - 172
19X-RAY DIFFRACTION1allJ1 - 108
20X-RAY DIFFRACTION1allK1 - 106
21X-RAY DIFFRACTION1allL1 - 213
22X-RAY DIFFRACTION1allM1 - 214
23X-RAY DIFFRACTION1allN1 - 216
24X-RAY DIFFRACTION1allO1 - 214
25X-RAY DIFFRACTION1allP1 - 181
26X-RAY DIFFRACTION1allQ1 - 204
27X-RAY DIFFRACTION1allR1 - 213
28X-RAY DIFFRACTION1allS1 - 211
29X-RAY DIFFRACTION1allT2 - 213
30X-RAY DIFFRACTION1allU1 - 211
31X-RAY DIFFRACTION1allV2 - 111
32X-RAY DIFFRACTION1allW1 - 105
33X-RAY DIFFRACTION1allX2 - 207
34X-RAY DIFFRACTION1allY1 - 109
35X-RAY DIFFRACTION1allZ1 - 205
36X-RAY DIFFRACTION1allz1 - 179
37X-RAY DIFFRACTION1allH - E101 - 403

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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