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- PDB-5nff: Crystal structure of GP1 receptor binding domain from Morogoro virus -

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基本情報

登録情報
データベース: PDB / ID: 5nff
タイトルCrystal structure of GP1 receptor binding domain from Morogoro virus
要素Glycoprotein
キーワードVIRAL PROTEIN / Viral envelope / receptor binding-domain / glycoprotein
機能・相同性
機能・相同性情報


host cell Golgi membrane / membrane => GO:0016020 / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding
類似検索 - 分子機能
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
類似検索 - ドメイン・相同性
CITRIC ACID / Pre-glycoprotein polyprotein GP complex
類似検索 - 構成要素
生物種Morogoro virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.615 Å
データ登録者Israeli, H. / Cohen-Dvashi, H. / Shulman, A. / Shimon, A. / Diskin, R.
資金援助 イスラエル, 1件
組織認可番号国
ISF - ICORE1775/12 イスラエル
引用ジャーナル: PLoS Pathog. / 年: 2017
タイトル: Mapping of the Lassa virus LAMP1 binding site reveals unique determinants not shared by other old world arenaviruses.
著者: Israeli, H. / Cohen-Dvashi, H. / Shulman, A. / Shimon, A. / Diskin, R.
履歴
登録2017年3月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年4月19日Provider: repository / タイプ: Initial release
改定 1.12017年5月10日Group: Database references
改定 1.22019年8月14日Group: Data collection / カテゴリ: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
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_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_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.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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年1月17日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: Glycoprotein
A: Glycoprotein
C: Glycoprotein
D: Glycoprotein
E: Glycoprotein
F: Glycoprotein
G: Glycoprotein
H: Glycoprotein
I: Glycoprotein
J: Glycoprotein
K: Glycoprotein
L: Glycoprotein
M: Glycoprotein
N: Glycoprotein
O: Glycoprotein
P: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)317,55041
ポリマ－310,57116
非ポリマー6,97925
水00
1
B: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,4705
ポリマ－19,4111
非ポリマー1,0594
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8533
ポリマ－19,4111
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0164
ポリマ－19,4111
非ポリマー6053
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,6322
ポリマ－19,4111
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0454
ポリマ－19,4111
非ポリマー6353
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0273
ポリマ－19,4111
非ポリマー6172
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8533
ポリマ－19,4111
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,3813
ポリマ－19,4111
非ポリマー9702
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8243
ポリマ－19,4111
非ポリマー4132
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
10
J: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,6322
ポリマ－19,4111
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
11
K: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,6322
ポリマ－19,4111
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
12
L: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,6322
ポリマ－19,4111
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
13
M: Glycoprotein


分子量 (理論値)分子数
合計 (水以外)19,4111
ポリマ－19,4111
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
14
N: Glycoprotein


分子量 (理論値)分子数
合計 (水以外)19,4111
ポリマ－19,4111
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
15
O: Glycoprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,3212
ポリマ－19,4111
非ポリマー9111
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
16
P: Glycoprotein


分子量 (理論値)分子数
合計 (水以外)19,4111
ポリマ－19,4111
非ポリマー00
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)127.769, 127.769, 251.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 80:86 or resseq 88:96 or resseq...
21(chain B and (resseq 80:86 or resseq 88:96 or resseq...
31(chain C and (resseq 80:86 or resseq 88:96 or resseq...
41(chain D and (resseq 80:86 or resseq 88:96 or resseq...
51(chain E and (resseq 80:86 or resseq 88:96 or resseq...
61(chain F and (resseq 80:86 or resseq 88:96 or resseq...
71(chain G and (resseq 80:86 or resseq 88:96 or resseq...
81(chain H and (resseq 80:86 or resseq 88:96 or resseq...
91(chain I and (resseq 80:86 or resseq 88:96 or resseq...
101(chain J and (resseq 80:86 or resseq 88:96 or resseq...
111(chain K and (resseq 80:86 or resseq 88:96 or resseq...
121(chain L and (resseq 80:86 or resseq 88:96 or resseq...
131(chain M and (resseq 80:86 or resseq 88:96 or resseq...
141(chain N and (resseq 80:86 or resseq 88:96 or resseq...
151(chain O and (resseq 80:86 or resseq 88:96 or resseq...
161(chain P and (resseq 80:86 or resseq 88:96 or resseq...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSER(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB80 - 8616 - 22
12ASNASNVALVAL(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB88 - 9624 - 32
13ASPASPASPASP(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB9935
14THRTHRTHRTHR(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB10036
15THRTHRSERSER(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB80 - 23516 - 171
16THRTHRSERSER(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB80 - 23516 - 171
17THRTHRSERSER(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB80 - 23516 - 171
18THRTHRSERSER(chain A and (resseq 80:86 or resseq 88:96 or resseq...AB80 - 23516 - 171
21THRTHRSERSER(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA80 - 8616 - 22
22ASNASNVALVAL(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA88 - 9624 - 32
23ASPASPASPASP(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA9935
24THRTHRTHRTHR(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA10036
25THRTHRSERSER(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA80 - 23516 - 171
26THRTHRSERSER(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA80 - 23516 - 171
27THRTHRSERSER(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA80 - 23516 - 171
28THRTHRSERSER(chain B and (resseq 80:86 or resseq 88:96 or resseq...BA80 - 23516 - 171
31THRTHRSERSER(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC80 - 8616 - 22
32ASNASNVALVAL(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC88 - 9624 - 32
33ASPASPASPASP(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC9935
34THRTHRTHRTHR(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC10036
35THRTHRSERSER(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC80 - 23516 - 171
36THRTHRSERSER(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC80 - 23516 - 171
37THRTHRSERSER(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC80 - 23516 - 171
38THRTHRSERSER(chain C and (resseq 80:86 or resseq 88:96 or resseq...CC80 - 23516 - 171
41THRTHRSERSER(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD80 - 8616 - 22
42ASNASNVALVAL(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD88 - 9624 - 32
43ASPASPASPASP(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD9935
44THRTHRTHRTHR(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD10036
45THRTHRSERSER(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD80 - 23516 - 171
46THRTHRSERSER(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD80 - 23516 - 171
47THRTHRSERSER(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD80 - 23516 - 171
48THRTHRSERSER(chain D and (resseq 80:86 or resseq 88:96 or resseq...DD80 - 23516 - 171
51THRTHRSERSER(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE80 - 8616 - 22
52ASNASNVALVAL(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE88 - 9624 - 32
53ASPASPASPASP(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE9935
54THRTHRTHRTHR(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE10036
55THRTHRSERSER(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE80 - 23516 - 171
56THRTHRSERSER(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE80 - 23516 - 171
57THRTHRSERSER(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE80 - 23516 - 171
58THRTHRSERSER(chain E and (resseq 80:86 or resseq 88:96 or resseq...EE80 - 23516 - 171
61THRTHRSERSER(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF80 - 8616 - 22
62ASNASNVALVAL(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF88 - 9624 - 32
63ASPASPASPASP(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF9935
64THRTHRTHRTHR(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF10036
65THRTHRSERSER(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF80 - 23516 - 171
66THRTHRSERSER(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF80 - 23516 - 171
67THRTHRSERSER(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF80 - 23516 - 171
68THRTHRSERSER(chain F and (resseq 80:86 or resseq 88:96 or resseq...FF80 - 23516 - 171
71THRTHRSERSER(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG80 - 8616 - 22
72ASNASNVALVAL(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG88 - 9624 - 32
73ASPASPASPASP(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG9935
74THRTHRTHRTHR(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG10036
75THRTHRSERSER(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG80 - 23516 - 171
76THRTHRSERSER(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG80 - 23516 - 171
77THRTHRSERSER(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG80 - 23516 - 171
78THRTHRSERSER(chain G and (resseq 80:86 or resseq 88:96 or resseq...GG80 - 23516 - 171
81THRTHRSERSER(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH80 - 8616 - 22
82ASNASNVALVAL(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH88 - 9624 - 32
83ASPASPASPASP(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH9935
84THRTHRTHRTHR(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH10036
85THRTHRSERSER(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH80 - 23516 - 171
86THRTHRSERSER(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH80 - 23516 - 171
87THRTHRSERSER(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH80 - 23516 - 171
88THRTHRSERSER(chain H and (resseq 80:86 or resseq 88:96 or resseq...HH80 - 23516 - 171
91THRTHRSERSER(chain I and (resseq 80:86 or resseq 88:96 or resseq...II80 - 8616 - 22
92ASNASNVALVAL(chain I and (resseq 80:86 or resseq 88:96 or resseq...II88 - 9624 - 32
93ASPASPASPASP(chain I and (resseq 80:86 or resseq 88:96 or resseq...II9935
94THRTHRTHRTHR(chain I and (resseq 80:86 or resseq 88:96 or resseq...II10036
95THRTHRSERSER(chain I and (resseq 80:86 or resseq 88:96 or resseq...II80 - 23516 - 171
96THRTHRSERSER(chain I and (resseq 80:86 or resseq 88:96 or resseq...II80 - 23516 - 171
97THRTHRSERSER(chain I and (resseq 80:86 or resseq 88:96 or resseq...II80 - 23516 - 171
98THRTHRSERSER(chain I and (resseq 80:86 or resseq 88:96 or resseq...II80 - 23516 - 171
101THRTHRSERSER(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ80 - 8616 - 22
102ASNASNVALVAL(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ88 - 9624 - 32
103ASPASPASPASP(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ9935
104THRTHRTHRTHR(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ10036
105THRTHRSERSER(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ80 - 23516 - 171
106THRTHRSERSER(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ80 - 23516 - 171
107THRTHRSERSER(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ80 - 23516 - 171
108THRTHRSERSER(chain J and (resseq 80:86 or resseq 88:96 or resseq...JJ80 - 23516 - 171
111THRTHRSERSER(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK80 - 8616 - 22
112ASNASNVALVAL(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK88 - 9624 - 32
113ASPASPASPASP(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK9935
114THRTHRTHRTHR(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK10036
115THRTHRSERSER(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK80 - 23516 - 171
116THRTHRSERSER(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK80 - 23516 - 171
117THRTHRSERSER(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK80 - 23516 - 171
118THRTHRSERSER(chain K and (resseq 80:86 or resseq 88:96 or resseq...KK80 - 23516 - 171
121THRTHRSERSER(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL80 - 8616 - 22
122ASNASNVALVAL(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL88 - 9624 - 32
123ASPASPASPASP(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL9935
124THRTHRTHRTHR(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL10036
125THRTHRSERSER(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL80 - 23516 - 171
126THRTHRSERSER(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL80 - 23516 - 171
127THRTHRSERSER(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL80 - 23516 - 171
128THRTHRSERSER(chain L and (resseq 80:86 or resseq 88:96 or resseq...LL80 - 23516 - 171
131THRTHRSERSER(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM80 - 8616 - 22
132ASNASNVALVAL(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM88 - 9624 - 32
133ASPASPASPASP(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM9935
134THRTHRTHRTHR(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM10036
135THRTHRSERSER(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM80 - 23516 - 171
136THRTHRSERSER(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM80 - 23516 - 171
137THRTHRSERSER(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM80 - 23516 - 171
138THRTHRSERSER(chain M and (resseq 80:86 or resseq 88:96 or resseq...MM80 - 23516 - 171
141THRTHRSERSER(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN80 - 8616 - 22
142ASNASNVALVAL(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN88 - 9624 - 32
143ASPASPASPASP(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN9935
144THRTHRTHRTHR(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN10036
145THRTHRSERSER(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN80 - 23516 - 171
146THRTHRSERSER(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN80 - 23516 - 171
147THRTHRSERSER(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN80 - 23516 - 171
148THRTHRSERSER(chain N and (resseq 80:86 or resseq 88:96 or resseq...NN80 - 23516 - 171
151THRTHRSERSER(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO80 - 8616 - 22
152ASNASNVALVAL(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO88 - 9624 - 32
153ASPASPASPASP(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO9935
154THRTHRTHRTHR(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO10036
155THRTHRSERSER(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO80 - 23516 - 171
156THRTHRSERSER(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO80 - 23516 - 171
157THRTHRSERSER(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO80 - 23516 - 171
158THRTHRSERSER(chain O and (resseq 80:86 or resseq 88:96 or resseq...OO80 - 23516 - 171
161THRTHRSERSER(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP80 - 8616 - 22
162ASNASNVALVAL(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP88 - 9624 - 32
163ASPASPASPASP(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP9935
164THRTHRTHRTHR(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP10036
165THRTHRSERSER(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP80 - 23516 - 171
166THRTHRSERSER(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP80 - 23516 - 171
167THRTHRSERSER(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP80 - 23516 - 171
168THRTHRSERSER(chain P and (resseq 80:86 or resseq 88:96 or resseq...PP80 - 23516 - 171

-
要素

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タンパク質 / 非ポリマー , 2種, 22分子 BACDEFGHIJKLMNOP

#1: タンパク質
Glycoprotein


分子量: 19410.670 Da / 分子数: 16 / 由来タイプ: 組換発現 / 由来: (組換発現) Morogoro virus (ウイルス) / 遺伝子: GPC / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: C6ZK00
#6: 化合物
ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H8O7

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糖 , 4種, 19分子

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


タイプ: oligosaccharide / 分子量: 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
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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: 15 / 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

-
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: 4.16 Å3/Da / 溶媒含有率: 70.46 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 26% PEG 8000, 100 mM sodium citrate pH 4.0 and 0.01% octylphenoxypolyethoxyethanol (IGEPAL)

-
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: ESRF / ビームライン: ID23-1 / 波長: 0.9194 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年11月27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: 0.9194 Å / 相対比: 1
反射解像度: 2.61→46.19 Å / Num. obs: 138414 / % possible obs: 98.9 % / 冗長度: 4 % / CC1/2: 0.987 / Rrim(I) all: 0.149 / Net I/σ(I): 9.09
反射 シェル解像度: 2.61→2.7 Å / 冗長度: 3.8 % / Mean I/σ(I) obs: 1.58 / CC1/2: 0.35 / Rrim(I) all: 0.963 / % possible all: 92.2

-
解析

ソフトウェア
名称バージョン分類
PHENIXdev_2236精密化
PDB_EXTRACT3.22データ抽出
XDSNovember 3, 2014データ削減
XSCALENovember 3, 2014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
開始モデル: 4ZJF

4zjf


解像度: 2.615→46.188 Å / SU ML: 0.26 / 交差検証法: FREE R-VALUE / σ(F): 2.3 / 位相誤差: 19.29
Rfactor反射数%反射Selection details
Rfree0.2074 6982 5.04 %Random
Rwork0.174 ---
obs0.1757 138413 99.65 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 149.88 Å2 / Biso mean: 55.7144 Å2 / Biso min: 18.69 Å2
精密化ステップサイクル: final / 解像度: 2.615→46.188 Å
タンパク質核酸リガンド溶媒全体
原子数19936 0 455 0 20391
Biso mean--68.52 --
残基数----2496
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00920941
X-RAY DIFFRACTIONf_angle_d1.1828554
X-RAY DIFFRACTIONf_chiral_restr0.073244
X-RAY DIFFRACTIONf_plane_restr0.0083612
X-RAY DIFFRACTIONf_dihedral_angle_d25.96111962
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A10415X-RAY DIFFRACTION14.012TORSIONAL
12B10415X-RAY DIFFRACTION14.012TORSIONAL
13C10415X-RAY DIFFRACTION14.012TORSIONAL
14D10415X-RAY DIFFRACTION14.012TORSIONAL
15E10415X-RAY DIFFRACTION14.012TORSIONAL
16F10415X-RAY DIFFRACTION14.012TORSIONAL
17G10415X-RAY DIFFRACTION14.012TORSIONAL
18H10415X-RAY DIFFRACTION14.012TORSIONAL
19I10415X-RAY DIFFRACTION14.012TORSIONAL
110J10415X-RAY DIFFRACTION14.012TORSIONAL
111K10415X-RAY DIFFRACTION14.012TORSIONAL
112L10415X-RAY DIFFRACTION14.012TORSIONAL
113M10415X-RAY DIFFRACTION14.012TORSIONAL
114N10415X-RAY DIFFRACTION14.012TORSIONAL
115O10415X-RAY DIFFRACTION14.012TORSIONAL
116P10415X-RAY DIFFRACTION14.012TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6149-2.64460.25782060.23763887409389
2.6446-2.67570.2422380.224144134651100
2.6757-2.70830.28082280.227644284656100
2.7083-2.74260.23012300.212843704600100
2.7426-2.77870.23982380.192444544692100
2.7787-2.81680.18622380.169943774615100
2.8168-2.8570.20322280.156743554583100
2.857-2.89960.20472280.161244414669100
2.8996-2.94490.22362380.15943724610100
2.9449-2.99320.20492140.156644154629100
2.9932-3.04480.20272560.153444164672100
3.0448-3.10020.21582220.165543874609100
3.1002-3.15980.19372120.159143994611100
3.1598-3.22430.17162230.158344034626100
3.2243-3.29440.22462340.177644264660100
3.2944-3.3710.1912380.160643834621100
3.371-3.45530.20873300.170543524682100
3.4553-3.54860.20122180.165343864604100
3.5486-3.6530.18011660.158144294595100
3.653-3.77090.20142740.157143944668100
3.7709-3.90560.18941740.15944064580100
3.9056-4.06190.18542430.169943704613100
4.0619-4.24660.21082300.174844644694100
4.2466-4.47030.19322730.155443194592100
4.4703-4.75020.18342180.146344234641100
4.7502-5.11650.18792560.155543864642100
5.1165-5.63060.19982440.167843854629100
5.6306-6.44340.23932240.204443994623100
6.4434-8.11090.23812240.203444114635100
8.1109-46.19490.24462370.233343814618100
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)
13.39960.40810.87564.60112.54214.63850.08370.10260.321-0.16990.0217-0.189-0.14410.0454-0.16070.3081-0.06640.04230.20.08920.31712.3263-4.157-42.9836
21.10250.3479-0.3231.1376-0.05261.42720.0050.00780.04740.01190.0286-0.1035-0.09240.0776-0.0310.2784-0.0577-0.00460.22780.01160.322810.3728-12.9091-38.6373
33.44181.7103-0.44926.67373.38542.70770.1142-0.2602-0.33140.463-0.0549-0.42-0.0688-0.0853-0.2130.33690.1364-0.0520.35260.01320.422882.585841.274239.2145
44.5171-4.8343-1.17419.46075.88865.2743-0.23210.3522-0.76420.27-0.5550.79150.9104-1.09970.94020.4959-0.03140.01330.3825-0.02450.640964.534941.218440.9722
50.70280.4592-0.37032.8426-1.11542.66340.1615-0.0672-0.0379-0.1611-0.12670.12980.09770.0976-0.03540.35730.08930.01430.2992-0.02750.414871.178651.081840.7371
66.3159-5.11420.90624.7243-1.61091.75520.10270.46350.5164-0.131-0.14740.0357-0.1335-0.10860.00810.39190.09070.01240.25380.0350.372375.037654.510328.3469
78.0183-5.00155.26426.2953-4.08226.95940.01191.0704-0.30080.3465-0.4749-0.0238-0.27330.86530.42990.47250.0118-0.00290.40590.05410.431680.740253.899624.1823
84.5753.88354.22663.3263.61874.3186-0.46110.21320.0398-0.77430.71030.4964-0.22380.5138-0.28180.3650.15040.09230.53390.01520.359774.856952.511725.5665
97.77910.96250.71242.8482-0.57442.8271-0.1195-0.4299-0.46130.4121-0.0027-0.41860.20840.31080.0840.42670.08340.01010.32180.02540.401578.96238.579642.1881
107.4273.4466-0.27072.3646-1.36464.39130.2102-0.05230.22480.1181-0.15130.3666-0.2869-0.2169-0.11360.29160.11070.06370.2614-0.02790.440291.478827.332539.1289
115.0196-1.26653.2872.95910.43954.22070.358-0.25880.10781.0904-0.7079-0.068-0.83321.17390.64630.4357-0.0801-0.03460.4526-0.02560.4596106.885126.114448.5641
122.3079-0.9533-0.23130.96020.73651.35750.0276-0.0745-0.23370.08940.00080.12610.2102-0.118-0.02520.34580.05130.04650.2150.07070.359100.761912.702842.6478
131.7754-0.7745-1.37441.13830.25432.76750.0539-0.0684-0.06150.04340.03260.12110.03750.1236-0.05630.26240.00060.03350.20610.02260.2816106.401121.378239.4129
149.0935-4.35036.57624.6488-4.2175.17620.05420.5022-0.15170.01050.0425-0.1221-0.13690.3997-0.05040.25260.03280.04490.18210.00290.31398.276317.179429.8197
150.8511-0.1601-0.64862.76061.63916.60860.17230.21680.0907-0.08430.0498-0.0892-0.1816-0.309-0.19320.15050.04660.00380.25840.05730.3152101.295720.936630.2933
167.4409-4.93184.62527.9226-7.82287.9353-0.5456-0.72740.28840.24020.17490.7708-0.7630.11590.3470.46810.09020.15320.2985-0.03120.331991.003831.19944.8836
177.858-5.62054.97436.8173-4.56553.522-0.01830.0308-1.038-0.54170.7744-0.50740.8652-0.9996-0.66970.4313-0.16050.02760.6599-0.05430.697470.424212.7462-6.8573
183.3774-3.2826-0.24496.45973.34785.1456-0.1311-0.76260.18040.41280.2906-0.0236-0.10641.2025-0.54090.2934-0.0353-0.03070.4728-0.05320.537361.622321.05860.7516
194.68155.4374-5.11826.0871-5.76585.4567-0.3434-0.8708-0.55170.1786-0.3721-0.55040.86350.75040.76060.49930.0244-0.09490.69260.04590.702956.00322.6950.8096
201.84810.42471.08221.39330.48682.46070.0038-0.310.00980.16240.0389-0.17960.06380.1121-0.05050.26540.009-0.01540.41780.00880.430150.490813.2631-0.6934
213.73421.68624.61840.6832.31389.4297-0.2782-0.00560.2129-0.16260.08210.0007-0.33470.03430.16840.20960.0505-0.03710.275-0.02550.419650.019217.4118-13.6124
227.8185-3.91414.38994.5458-1.37999.235-0.12290.13530.9897-0.1070.069-0.5631-0.42070.2807-0.03210.2742-0.00130.00740.2055-0.02180.351953.271321.4764-17.795
238.9666-7.92371.75047.5697-0.63232.60060.3041-0.1664-0.1557-0.2001-0.03260.09010.0769-0.017-0.32030.2135-0.10110.03090.296-0.02420.438951.622215.8496-16.1933
247.92672.18770.21636.08624.3746.5667-0.1329-0.54430.40210.7426-0.0148-0.26610.37010.29470.07960.35990.0613-0.08460.43530.00340.383165.110814.10291.4332
254.5593-3.70910.69115.65510.31291.4731-0.06220.0825-0.2120.1378-0.08050.2225-0.0006-0.15530.06560.231-0.049-0.02690.4334-0.02930.381581.122619.4386-1.3255
262.9872-4.90062.66118.9404-4.47032.2797-0.6729-0.43140.75160.82920.193-0.5919-0.6219-0.66150.64280.43810.00940.02970.5117-0.01690.526190.481732.63197.091
271.83750.1658-0.2110.6133-0.25240.82360.0225-0.0321-0.17350.0312-0.0415-0.12550.03010.03690.0060.22390.0058-0.03640.29870.03630.311196.884621.38052.8178
283.4692-0.55541.10158.3834-7.82519.086-0.24020.0994-0.03790.0064-0.093-0.5734-0.0779-0.17830.51190.264-0.0362-0.00990.35850.04090.469591.176529.0789-2.1048
297.99596.1852.14544.59982.12535.306-0.23970.30330.0402-0.44820.4242-0.22970.01950.4904-0.09040.25680.0595-0.01250.38860.03470.392495.976524.407-11.7424
305.7452-3.2312-5.13856.08242.81074.61770.2215-0.2607-0.0619-0.1789-0.1456-0.14220.0804-0.1686-0.07380.322-0.0335-0.07230.46680.0910.357693.266324.1186-15.7123
316.49135.4724-1.03344.3226-0.75021.7201-0.016-0.0338-0.11220.0842-0.10840.00940.1218-0.2960.08380.26350.0252-0.00260.44450.05270.405280.731721.97323.1974
324.6052-0.6312.0672.4886-0.59194.714-0.01410.20860.1143-0.08540.0945-0.4602-0.13320.3086-0.12760.1961-0.03430.10490.32840.03040.3739125.560123.7769-2.4094
331.3162-0.042-0.52710.65840.21960.78420.01860.1295-0.0456-0.09240.01450.0014-0.04420.1913-0.02750.2666-0.01470.00410.38870.01390.3418117.289521.55652.6143
346.32192.88452.90115.40775.53885.7375-0.1510.0895-0.7676-0.70050.4990.4516-1.69790.267-0.22070.4496-0.0561-0.02330.36840.04490.58830.84251.21-40.2387
351.5495-2.4128-0.09386.5583-3.31165.41150.02020.0649-0.0408-0.36480.13890.5253-0.0296-0.2414-0.33590.4552-0.0876-0.07620.3479-0.01330.493325.458114.3368-43.3843
368.03946.0234-5.97195.8129-4.96094.4771-0.5530.8874-0.171-0.97680.2751-0.2611.24660.740.08040.62950.02690.04730.4994-0.12540.465342.388110.9448-52.3289
373.00310.16940.56680.40460.86173.0259-0.1240.34210.0404-0.35720.14420.1315-0.0792-0.0947-0.01750.4476-0.0846-0.0290.28830.06450.502636.539822.3217-47.4365
381.65580.46810.5701-0.08120.62093.77230.234-0.0973-0.1005-0.1393-0.04730.01960.0355-0.0027-0.15280.3873-0.055-0.03940.2662-0.00390.457840.331517.7706-36.5925
392.13492.46711.48196.71360.31924.92650.3063-0.26440.05040.2776-0.11050.18930.0743-0.3916-0.18720.1459-0.03840.00950.31370.00350.3737.213916.0279-33.5624
408.58631.0013-0.32576.1291-0.55078.6435-0.19670.059-0.66550.7817-0.28230.23720.82580.43160.3990.4208-0.0328-0.06490.28250.03590.40626.52886.0593-48.1851
415.37021.1368-4.22732.4576-1.30926.0668-0.27020.2399-0.2857-0.14110.13670.20050.3457-0.49870.14350.245-0.0275-0.10190.39590.01490.452720.362112.9863-4.6118
420.9211-0.4443-0.42241.1864-0.1670.8996-0.0685-0.1706-0.01730.08060.0849-0.00880.0783-0.0545-0.00440.2877-0.0196-0.01460.45840.04470.446128.743113.47910.7118
436.8628-2.61311.45047.4901-0.04214.4486-0.0221-0.6797-0.36620.04230.11490.32390.3193-0.4242-0.16790.2229-0.06620.03240.50460.08230.357257.480874.6869-3.5618
449.7947-6.94957.02359.5109-5.51564.8547-1.1603-0.83910.31251.74710.4604-0.4736-0.9748-0.60760.48910.5663-0.02440.09020.6981-0.02630.471566.234486.2066.9472
451.4254-0.0674-0.20011.22520.34060.71250.0265-0.2427-0.04670.14220.0056-0.15040.07780.0812-0.03270.2681-0.01-0.04340.40190.05990.347471.968179.0568-3.5453
465.5083-3.3072-3.53382.3511.8114.1695-0.1371-0.18260.08970.15940.3005-0.30810.10670.0691-0.18450.3167-0.0048-0.04660.32190.04270.340469.997281.9299-16.5438
479.53346.8009-0.78744.97990.06544.39740.1867-0.0648-0.46110.2058-0.1855-0.29420.1337-0.64480.00190.28880.0107-0.02170.55110.12470.406656.977376.30861.3619
485.064-3.4007-6.62895.3143.79839.178-0.1304-0.28520.10270.18440.1623-0.2647-0.00680.4501-0.230.2188-0.0742-0.06680.48320.04490.359840.9873.7242-3.3292
491.53011.4086-0.02021.473-0.26233.0459-0.0384-0.0344-0.11780.0489-0.0192-0.08510.23210.09170.09350.220.0330.0070.3822-0.0020.306526.197267.5797-1.4498
500.9340.2468-1.16373.8919-2.25914.40860.01660.1050.1349-0.0882-0.10590.0249-0.09920.15490.11340.24290.0334-0.02890.4631-0.01450.329728.006572.8183-12.2528
517.78280.38054.37168.06370.39184.324-0.0378-0.35160.12570.4939-0.2042-0.23930.13230.08920.19880.2398-0.00550.00270.4480.01090.222840.591268.8762-3.0692
527.28034.733-3.32818.6572-1.26612.6190.04010.1020.4142-0.2385-0.17710.4485-0.2469-0.01110.05560.22980.0484-0.08840.32010.0360.2941-6.403673.8827-1.8507
533.25523.5005-1.06097.6428-4.73524.3229-0.43370.6735-0.5099-1.0155-0.0073-0.21661.0747-0.28950.50940.48910.0364-0.04950.437-0.06150.40442.327162.1079-12.3177
541.557-1.52961.79731.9825-0.61532.3568-0.0450.32040.284-0.1801-0.1525-0.1882-0.13950.32860.18260.2115-0.04820.04240.32130.03720.265110.822973.4266-4.8544
550.4987-0.71431.22132.4626-2.78288.78320.11340.24110.138-0.36060.03170.00350.42320.2671-0.12270.2051-0.0033-0.00170.32710.05090.33916.030863.908-2.5647
562.1277-2.29610.37638.69160.9738.0262-0.3495-0.20440.01470.48340.1484-0.02180.060.43660.24960.2197-0.01-0.00530.26630.03430.28875.267170.359710.4783
572.10871.22961.76773.4321-0.35945.10320.00020.0174-0.02060.11380.2099-0.08630.10940.242-0.21130.14980.05620.03550.32510.020.28782.633767.15322.3933
586.9046-4.4302-4.74664.74894.79224.93060.1866-0.18850.2044-0.7198-0.2909-0.111-0.4684-0.10650.14130.34020.047-0.03390.37950.08050.3873-10.127573.149-7.7132
596.8491-1.20146.32151.6558-0.9466.8372-0.2088-0.0860.18120.21850.1719-0.31310.0122-0.1834-0.01350.2199-0.04610.0890.41680.04220.3249101.788179.8724-2.1054
602.0252-0.36510.42521.080.27221.8854-0.0121-0.0939-0.09410.09370.08420.05880.0817-0.266-0.06280.283-0.0127-0.01370.40010.0430.332193.36676.71672.0279
614.1571-2.8391-3.54645.92533.72975.97780.2194-0.0736-0.0358-0.20120.1247-0.32040.34850.3422-0.56850.4310.114-0.06010.36650.05760.39716.428242.592738.0915
625.9109-5.9908-6.9127.54126.43668.654-0.38660.4008-1.03290.4811-0.47040.84940.5092-1.15650.92490.42920.0221-0.03860.4992-0.00820.6651-1.648942.489639.036
631.0842-0.2379-0.33410.02640.04293.157-0.0412-0.2478-0.07850.07360.0712-0.0960.3988-0.0182-0.01750.39650.0713-0.02520.29350.0220.36464.729353.014836.2651
645.6704-6.4157-6.20897.69226.39447.8546-0.24291.04650.4734-0.1259-0.1571-0.0506-0.273-0.55340.35870.30150.0239-0.06560.25940.04590.247514.797754.941529.2808
652.25560.36040.05064.7238-3.32944.4780.1420.1665-0.10060.15620.0479-0.25910.12470.4683-0.17310.32230.0474-0.0340.3057-0.06510.319412.043551.618627.371
668.55994.64633.33273.45482.60442.2851-0.0459-0.6441-0.53990.2660.05120.2372-0.112-0.4153-0.03760.69650.14570.01510.47080.10650.59414.581137.350742.2294
671.23150.87790.73993.07490.31982.78080.04720.2531-0.0289-0.5416-0.00820.0799-0.1063-0.1946-0.03890.67420.1768-0.03490.4679-0.07270.430749.2261-5.053236.1171
682.9566-2.13920.25652.149-1.15812.9240.27210.4648-0.1130.106-0.24170.04290.8415-0.2176-0.06560.59860.148-0.03950.4007-0.05810.33139.35235.622244.1587
694.94545.08485.33235.78645.13075.94640.22591.2101-0.2919-0.8183-0.5298-0.46411.25721.12860.30210.91290.2729-0.01320.6403-0.01450.552855.04630.28532.6821
701.1064-0.5662-1.1744.58642.4512.9037-0.04650.0288-0.0989-0.1251-0.06830.45680.0817-0.0770.12280.47930.1458-0.08120.4372-0.02560.382345.1701-3.980446.4678
713.2291-3.35571.01866.3911-1.79053.03290.36220.5039-0.43630.0525-0.40710.28940.3149-0.0098-0.10180.3805-0.0877-0.04270.3286-0.05590.4718-4.139162.1362-45.4799
727.10395.1025-5.6034.5355-4.46284.30710.18090.7520.0095-0.3698-0.25420.32380.38690.8046-0.11140.46430.0089-0.06030.4641-0.03840.338610.742364.2898-55.3306
731.42041.09610.31131.07620.95881.0988-0.0487-0.02970.12970.12520.03210.0381-0.05390.0257-0.0180.4446-0.0601-0.05980.32660.06990.36114.693977.106-48.2037
744.40841.37674.15314.73131.46934.19920.1096-0.35230.43920.1936-0.35510.08460.2857-0.67780.11790.3591-0.0155-0.00360.38690.02810.37727.820466.1265-50.325
756.03341.24931.89661.68310.85383.0712-0.1247-0.3296-0.13170.2740.0491-0.0296-0.03760.29340.04220.4011-0.0396-0.03810.24680.00420.28478.713372.1141-35.867
763.71360.0992.69615.37472.46982.89180.1819-0.7044-0.14130.3045-0.15370.06650.0038-0.1765-0.08540.4723-0.0708-0.0680.44580.03870.30717.629569.6462-31.9258
777.75382.3681-1.68962.6805-1.01316.2372-0.36180.1811-0.1809-0.31740.38610.28810.6506-0.5601-0.05390.4731-0.0221-0.05060.32540.05610.4123-2.512760.8307-50.4294
783.19683.0572-0.65448.5683-1.1575.98760.2336-0.0210.0448-0.1283-0.12980.1762-0.2479-0.4572-0.20040.46540.1407-0.02360.373-0.00740.506225.334728.60538.4784
791.562-1.23860.43697.1107-5.74655.83910.0113-0.0726-0.24350.20230.11830.0293-0.02170.1786-0.19410.48360.1230.01950.3853-0.02540.472135.03620.09947.3632
806.4336-5.3234-0.53236.7369-0.030.0899-0.10380.4497-0.7738-0.7757-0.05740.40490.48570.16890.17980.92460.07-0.0580.52240.07270.388738.979112.761434.5963
818.0936.0105-6.71389.5284-7.03849.6775-0.3503-0.0762-0.1023-0.1313-0.0784-0.66410.96680.32410.40210.5560.1692-0.08440.4136-0.02440.495337.449324.722643.1659
829.2314-2.837-0.90895.09-1.7541.31060.37330.9220.7989-0.3275-0.46080.1119-0.14830.12940.05611.00570.2608-0.09550.6099-0.05030.506839.017618.720928.7608
833.85692.2566-1.06168.76576.67847.3316-0.13650.2542-0.1516-0.63520.2232-0.00790.16330.3257-0.14640.61690.131-0.03260.50420.02480.430236.572121.131324.89
849.1808-1.122-2.10293.83-0.88794.61570.0031-0.152-0.0111-0.0197-0.21980.2945-0.3613-0.32630.15770.42510.0578-0.06790.3051-0.01670.421527.001230.087243.2772
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 80 through 121 )B80 - 121
2X-RAY DIFFRACTION2chain 'B' and (resid 122 through 235 )B122 - 235
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 107 )A80 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 121 )A108 - 121
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 171 )A122 - 171
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 193 )A172 - 193
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 205 )A194 - 205
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 216 )A206 - 216
9X-RAY DIFFRACTION9chain 'A' and (resid 217 through 235 )A217 - 235
10X-RAY DIFFRACTION10chain 'C' and (resid 80 through 107 )C80 - 107
11X-RAY DIFFRACTION11chain 'C' and (resid 108 through 121 )C108 - 121
12X-RAY DIFFRACTION12chain 'C' and (resid 122 through 151 )C122 - 151
13X-RAY DIFFRACTION13chain 'C' and (resid 152 through 181 )C152 - 181
14X-RAY DIFFRACTION14chain 'C' and (resid 182 through 193 )C182 - 193
15X-RAY DIFFRACTION15chain 'C' and (resid 194 through 224 )C194 - 224
16X-RAY DIFFRACTION16chain 'C' and (resid 225 through 235 )C225 - 235
17X-RAY DIFFRACTION17chain 'D' and (resid 80 through 89 )D80 - 89
18X-RAY DIFFRACTION18chain 'D' and (resid 90 through 107 )D90 - 107
19X-RAY DIFFRACTION19chain 'D' and (resid 108 through 121 )D108 - 121
20X-RAY DIFFRACTION20chain 'D' and (resid 122 through 171 )D122 - 171
21X-RAY DIFFRACTION21chain 'D' and (resid 172 through 193 )D172 - 193
22X-RAY DIFFRACTION22chain 'D' and (resid 194 through 205 )D194 - 205
23X-RAY DIFFRACTION23chain 'D' and (resid 206 through 216 )D206 - 216
24X-RAY DIFFRACTION24chain 'D' and (resid 217 through 235 )D217 - 235
25X-RAY DIFFRACTION25chain 'E' and (resid 80 through 107 )E80 - 107
26X-RAY DIFFRACTION26chain 'E' and (resid 108 through 121 )E108 - 121
27X-RAY DIFFRACTION27chain 'E' and (resid 122 through 159 )E122 - 159
28X-RAY DIFFRACTION28chain 'E' and (resid 160 through 171 )E160 - 171
29X-RAY DIFFRACTION29chain 'E' and (resid 172 through 193 )E172 - 193
30X-RAY DIFFRACTION30chain 'E' and (resid 194 through 216 )E194 - 216
31X-RAY DIFFRACTION31chain 'E' and (resid 217 through 235 )E217 - 235
32X-RAY DIFFRACTION32chain 'F' and (resid 80 through 121 )F80 - 121
33X-RAY DIFFRACTION33chain 'F' and (resid 122 through 235 )F122 - 235
34X-RAY DIFFRACTION34chain 'G' and (resid 80 through 89 )G80 - 89
35X-RAY DIFFRACTION35chain 'G' and (resid 90 through 107 )G90 - 107
36X-RAY DIFFRACTION36chain 'G' and (resid 108 through 121 )G108 - 121
37X-RAY DIFFRACTION37chain 'G' and (resid 122 through 159 )G122 - 159
38X-RAY DIFFRACTION38chain 'G' and (resid 160 through 193 )G160 - 193
39X-RAY DIFFRACTION39chain 'G' and (resid 194 through 224 )G194 - 224
40X-RAY DIFFRACTION40chain 'G' and (resid 225 through 235 )G225 - 235
41X-RAY DIFFRACTION41chain 'H' and (resid 80 through 121 )H80 - 121
42X-RAY DIFFRACTION42chain 'H' and (resid 122 through 235 )H122 - 235
43X-RAY DIFFRACTION43chain 'I' and (resid 80 through 107 )I80 - 107
44X-RAY DIFFRACTION44chain 'I' and (resid 108 through 121 )I108 - 121
45X-RAY DIFFRACTION45chain 'I' and (resid 122 through 193 )I122 - 193
46X-RAY DIFFRACTION46chain 'I' and (resid 194 through 216 )I194 - 216
47X-RAY DIFFRACTION47chain 'I' and (resid 217 through 235 )I217 - 235
48X-RAY DIFFRACTION48chain 'J' and (resid 80 through 107 )J80 - 107
49X-RAY DIFFRACTION49chain 'J' and (resid 108 through 151 )J108 - 151
50X-RAY DIFFRACTION50chain 'J' and (resid 152 through 213 )J152 - 213
51X-RAY DIFFRACTION51chain 'J' and (resid 214 through 235 )J214 - 235
52X-RAY DIFFRACTION52chain 'K' and (resid 80 through 107 )K80 - 107
53X-RAY DIFFRACTION53chain 'K' and (resid 108 through 121 )K108 - 121
54X-RAY DIFFRACTION54chain 'K' and (resid 122 through 151 )K122 - 151
55X-RAY DIFFRACTION55chain 'K' and (resid 152 through 181 )K152 - 181
56X-RAY DIFFRACTION56chain 'K' and (resid 182 through 205 )K182 - 205
57X-RAY DIFFRACTION57chain 'K' and (resid 206 through 224 )K206 - 224
58X-RAY DIFFRACTION58chain 'K' and (resid 225 through 235 )K225 - 235
59X-RAY DIFFRACTION59chain 'L' and (resid 80 through 121 )L80 - 121
60X-RAY DIFFRACTION60chain 'L' and (resid 122 through 235 )L122 - 235
61X-RAY DIFFRACTION61chain 'M' and (resid 80 through 107 )M80 - 107
62X-RAY DIFFRACTION62chain 'M' and (resid 108 through 121 )M108 - 121
63X-RAY DIFFRACTION63chain 'M' and (resid 122 through 181 )M122 - 181
64X-RAY DIFFRACTION64chain 'M' and (resid 182 through 193 )M182 - 193
65X-RAY DIFFRACTION65chain 'M' and (resid 194 through 224 )M194 - 224
66X-RAY DIFFRACTION66chain 'M' and (resid 225 through 235 )M225 - 235
67X-RAY DIFFRACTION67chain 'N' and (resid 80 through 138 )N80 - 138
68X-RAY DIFFRACTION68chain 'N' and (resid 139 through 151 )N139 - 151
69X-RAY DIFFRACTION69chain 'N' and (resid 152 through 159 )N152 - 159
70X-RAY DIFFRACTION70chain 'N' and (resid 160 through 235 )N160 - 235
71X-RAY DIFFRACTION71chain 'O' and (resid 80 through 107 )O80 - 107
72X-RAY DIFFRACTION72chain 'O' and (resid 108 through 121 )O108 - 121
73X-RAY DIFFRACTION73chain 'O' and (resid 122 through 151 )O122 - 151
74X-RAY DIFFRACTION74chain 'O' and (resid 152 through 171 )O152 - 171
75X-RAY DIFFRACTION75chain 'O' and (resid 172 through 193 )O172 - 193
76X-RAY DIFFRACTION76chain 'O' and (resid 194 through 216 )O194 - 216
77X-RAY DIFFRACTION77chain 'O' and (resid 217 through 235 )O217 - 235
78X-RAY DIFFRACTION78chain 'P' and (resid 80 through 107 )P80 - 107
79X-RAY DIFFRACTION79chain 'P' and (resid 108 through 138 )P108 - 138
80X-RAY DIFFRACTION80chain 'P' and (resid 139 through 151 )P139 - 151
81X-RAY DIFFRACTION81chain 'P' and (resid 152 through 171 )P152 - 171
82X-RAY DIFFRACTION82chain 'P' and (resid 172 through 192 )P172 - 192
83X-RAY DIFFRACTION83chain 'P' and (resid 193 through 216 )P193 - 216
84X-RAY DIFFRACTION84chain 'P' and (resid 217 through 235 )P217 - 235

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万見について

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る