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- PDB-7k6v: Crystal Structure of Virus-like Particles of GII.4 Norovirus Hous... -

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基本情報

登録情報
データベース: PDB / ID: 7k6v
タイトルCrystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus (HOV)
要素Capsid protein VP1
キーワードVIRUS LIKE PARTICLE / Norovirus / capsid protein / Houston virus
機能・相同性Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / : / VP1
機能・相同性情報
生物種Norovirus Hu/Houston/TCH186/2002/US (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Hu, L. / Prasad, B.V.V.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 米国
引用ジャーナル: To Be Published
タイトル: Crystal structure of GII.4 Norovirus capsid reveals inherent conformational flexibility of the capsid protein
著者: Hu, L. / Prasad, B.V.V.
履歴
登録2020年9月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年3月2日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

ダウンロードとリンク

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集合体

登録構造単位
AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,648,548118
ポリマ－2,644,24045
非ポリマー4,30873
水543
1
AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
ヘテロ分子

AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
ヘテロ分子

AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
ヘテロ分子

AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,594,192472
ポリマ－10,576,961180
非ポリマー17,231292
水21612
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
単位格子
Length a, b, c (Å)420.170, 446.597, 463.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301
311
321
331
341
351
361
371
381
391
401
411
421
431
441
451

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
11ALAALAARGARG(chain 'AA' and (resid 28 through 220 or (resid 221...AAA28 - 18728 - 187
12VALVALASNASN(chain 'AA' and (resid 28 through 220 or (resid 221...AAA195 - 302195 - 302
13ASNASNARGARG(chain 'AA' and (resid 28 through 220 or (resid 221...AAA310 - 435310 - 435
14CYSCYSALAALA(chain 'AA' and (resid 28 through 220 or (resid 221...AAA451 - 528451 - 528
21ALAALAARGARG(chain 'AB' and (resid 28 through 188 or resid 195...ABB28 - 18728 - 187
22VALVALASNASN(chain 'AB' and (resid 28 through 188 or resid 195...ABB195 - 302195 - 302
23ASNASNARGARG(chain 'AB' and (resid 28 through 188 or resid 195...ABB310 - 435310 - 435
24CYSCYSALAALA(chain 'AB' and (resid 28 through 188 or resid 195...ABB451 - 528451 - 528
31ALAALAARGARG(chain 'AC' and (resid 28 through 188 or resid 195...ACC28 - 18728 - 187
32VALVALASNASN(chain 'AC' and (resid 28 through 188 or resid 195...ACC195 - 302195 - 302
33ASNASNARGARG(chain 'AC' and (resid 28 through 188 or resid 195...ACC310 - 435310 - 435
34CYSCYSALAALA(chain 'AC' and (resid 28 through 188 or resid 195...ACC451 - 528451 - 528
41ALAALAARGARG(chain 'BA' and (resid 28 through 220 or (resid 221...BAD28 - 18728 - 187
42VALVALASNASN(chain 'BA' and (resid 28 through 220 or (resid 221...BAD195 - 302195 - 302
43ASNASNARGARG(chain 'BA' and (resid 28 through 220 or (resid 221...BAD310 - 435310 - 435
44CYSCYSALAALA(chain 'BA' and (resid 28 through 220 or (resid 221...BAD451 - 528451 - 528
51ALAALAARGARG(chain 'BB' and (resid 28 through 188 or resid 195...BBE28 - 18728 - 187
52VALVALASNASN(chain 'BB' and (resid 28 through 188 or resid 195...BBE195 - 302195 - 302
53ASNASNARGARG(chain 'BB' and (resid 28 through 188 or resid 195...BBE310 - 435310 - 435
54CYSCYSALAALA(chain 'BB' and (resid 28 through 188 or resid 195...BBE451 - 528451 - 528
61ALAALAARGARG(chain 'BC' and (resid 28 through 188 or resid 195...BCF28 - 18728 - 187
62VALVALASNASN(chain 'BC' and (resid 28 through 188 or resid 195...BCF195 - 302195 - 302
63ASNASNARGARG(chain 'BC' and (resid 28 through 188 or resid 195...BCF310 - 435310 - 435
64CYSCYSALAALA(chain 'BC' and (resid 28 through 188 or resid 195...BCF451 - 528451 - 528
71ALAALAARGARG(chain 'CA' and (resid 28 through 220 or (resid 221...CAG28 - 18728 - 187
72VALVALASNASN(chain 'CA' and (resid 28 through 220 or (resid 221...CAG195 - 302195 - 302
73ASNASNARGARG(chain 'CA' and (resid 28 through 220 or (resid 221...CAG310 - 435310 - 435
74CYSCYSALAALA(chain 'CA' and (resid 28 through 220 or (resid 221...CAG451 - 528451 - 528
81ALAALAARGARG(chain 'CB' and (resid 28 through 188 or resid 195...CBH28 - 18728 - 187
82VALVALASNASN(chain 'CB' and (resid 28 through 188 or resid 195...CBH195 - 302195 - 302
83ASNASNARGARG(chain 'CB' and (resid 28 through 188 or resid 195...CBH310 - 435310 - 435
84CYSCYSALAALA(chain 'CB' and (resid 28 through 188 or resid 195...CBH451 - 528451 - 528
91ALAALAARGARG(chain 'CC' and (resid 28 through 188 or resid 195...CCI28 - 18728 - 187
92VALVALASNASN(chain 'CC' and (resid 28 through 188 or resid 195...CCI195 - 302195 - 302
93ASNASNARGARG(chain 'CC' and (resid 28 through 188 or resid 195...CCI310 - 435310 - 435
94CYSCYSALAALA(chain 'CC' and (resid 28 through 188 or resid 195...CCI451 - 528451 - 528
101ALAALAARGARG(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ28 - 18728 - 187
102VALVALASNASN(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ195 - 302195 - 302
103ASNASNARGARG(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ310 - 435310 - 435
104CYSCYSALAALA(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ451 - 528451 - 528
111ALAALAARGARG(chain 'DB' and (resid 28 through 188 or resid 195...DBK28 - 18728 - 187
112VALVALASNASN(chain 'DB' and (resid 28 through 188 or resid 195...DBK195 - 302195 - 302
113ASNASNARGARG(chain 'DB' and (resid 28 through 188 or resid 195...DBK310 - 435310 - 435
114CYSCYSALAALA(chain 'DB' and (resid 28 through 188 or resid 195...DBK451 - 528451 - 528
121ALAALAARGARG(chain 'DC' and (resid 28 through 188 or resid 195...DCL28 - 18728 - 187
122VALVALASNASN(chain 'DC' and (resid 28 through 188 or resid 195...DCL195 - 302195 - 302
123ASNASNARGARG(chain 'DC' and (resid 28 through 188 or resid 195...DCL310 - 435310 - 435
124CYSCYSALAALA(chain 'DC' and (resid 28 through 188 or resid 195...DCL451 - 528451 - 528
131ALAALAARGARG(chain 'EA' and (resid 28 through 220 or (resid 221...EAM28 - 18728 - 187
132VALVALASNASN(chain 'EA' and (resid 28 through 220 or (resid 221...EAM195 - 302195 - 302
133ASNASNARGARG(chain 'EA' and (resid 28 through 220 or (resid 221...EAM310 - 435310 - 435
134CYSCYSALAALA(chain 'EA' and (resid 28 through 220 or (resid 221...EAM451 - 528451 - 528
141ALAALAARGARG(chain 'EB' and (resid 28 through 188 or resid 195...EBN28 - 18728 - 187
142VALVALASNASN(chain 'EB' and (resid 28 through 188 or resid 195...EBN195 - 302195 - 302
143ASNASNARGARG(chain 'EB' and (resid 28 through 188 or resid 195...EBN310 - 435310 - 435
144CYSCYSALAALA(chain 'EB' and (resid 28 through 188 or resid 195...EBN451 - 528451 - 528
151ALAALAARGARG(chain 'EC' and (resid 28 through 188 or resid 195...ECO28 - 18728 - 187
152VALVALASNASN(chain 'EC' and (resid 28 through 188 or resid 195...ECO195 - 302195 - 302
153ASNASNARGARG(chain 'EC' and (resid 28 through 188 or resid 195...ECO310 - 435310 - 435
154CYSCYSALAALA(chain 'EC' and (resid 28 through 188 or resid 195...ECO451 - 528451 - 528
161ALAALAARGARG(chain 'FA' and (resid 28 through 220 or (resid 221...FAP28 - 18728 - 187
162VALVALASNASN(chain 'FA' and (resid 28 through 220 or (resid 221...FAP195 - 302195 - 302
163ASNASNARGARG(chain 'FA' and (resid 28 through 220 or (resid 221...FAP310 - 435310 - 435
164CYSCYSALAALA(chain 'FA' and (resid 28 through 220 or (resid 221...FAP451 - 528451 - 528
171ALAALAARGARG(chain 'FB' and (resid 28 through 188 or resid 195...FBQ28 - 18728 - 187
172VALVALASNASN(chain 'FB' and (resid 28 through 188 or resid 195...FBQ195 - 302195 - 302
173ASNASNARGARG(chain 'FB' and (resid 28 through 188 or resid 195...FBQ310 - 435310 - 435
174CYSCYSALAALA(chain 'FB' and (resid 28 through 188 or resid 195...FBQ451 - 528451 - 528
181ALAALAARGARG(chain 'FC' and (resid 28 through 188 or resid 195...FCR28 - 18728 - 187
182VALVALASNASN(chain 'FC' and (resid 28 through 188 or resid 195...FCR195 - 302195 - 302
183ASNASNARGARG(chain 'FC' and (resid 28 through 188 or resid 195...FCR310 - 435310 - 435
184CYSCYSALAALA(chain 'FC' and (resid 28 through 188 or resid 195...FCR451 - 528451 - 528
191ALAALAARGARG(chain 'GA' and (resid 28 through 220 or (resid 221...GAS28 - 18728 - 187
192VALVALASNASN(chain 'GA' and (resid 28 through 220 or (resid 221...GAS195 - 302195 - 302
193ASNASNARGARG(chain 'GA' and (resid 28 through 220 or (resid 221...GAS310 - 435310 - 435
194CYSCYSALAALA(chain 'GA' and (resid 28 through 220 or (resid 221...GAS451 - 528451 - 528
201ALAALAARGARG(chain 'GB' and (resid 28 through 188 or resid 195...GBT28 - 18728 - 187
202VALVALASNASN(chain 'GB' and (resid 28 through 188 or resid 195...GBT195 - 302195 - 302
203ASNASNARGARG(chain 'GB' and (resid 28 through 188 or resid 195...GBT310 - 435310 - 435
204CYSCYSALAALA(chain 'GB' and (resid 28 through 188 or resid 195...GBT451 - 528451 - 528
211ALAALAARGARG(chain 'GC' and (resid 28 through 188 or resid 195...GCU28 - 18728 - 187
212VALVALASNASN(chain 'GC' and (resid 28 through 188 or resid 195...GCU195 - 302195 - 302
213ASNASNARGARG(chain 'GC' and (resid 28 through 188 or resid 195...GCU310 - 435310 - 435
214CYSCYSALAALA(chain 'GC' and (resid 28 through 188 or resid 195...GCU451 - 528451 - 528
221ALAALAARGARG(chain 'HA' and (resid 28 through 220 or (resid 221...HAV28 - 18728 - 187
222VALVALASNASN(chain 'HA' and (resid 28 through 220 or (resid 221...HAV195 - 302195 - 302
223ASNASNARGARG(chain 'HA' and (resid 28 through 220 or (resid 221...HAV310 - 435310 - 435
224CYSCYSALAALA(chain 'HA' and (resid 28 through 220 or (resid 221...HAV451 - 528451 - 528
231ALAALAARGARG(chain 'HB' and (resid 28 through 188 or resid 195...HBW28 - 18728 - 187
232VALVALASNASN(chain 'HB' and (resid 28 through 188 or resid 195...HBW195 - 302195 - 302
233ASNASNARGARG(chain 'HB' and (resid 28 through 188 or resid 195...HBW310 - 435310 - 435
234CYSCYSALAALA(chain 'HB' and (resid 28 through 188 or resid 195...HBW451 - 528451 - 528
241ALAALAARGARG(chain 'HC' and (resid 28 through 188 or resid 195...HCX28 - 18728 - 187
242VALVALASNASN(chain 'HC' and (resid 28 through 188 or resid 195...HCX195 - 302195 - 302
243ASNASNARGARG(chain 'HC' and (resid 28 through 188 or resid 195...HCX310 - 435310 - 435
244CYSCYSALAALA(chain 'HC' and (resid 28 through 188 or resid 195...HCX451 - 528451 - 528
251ALAALAARGARG(chain 'IA' and (resid 28 through 220 or (resid 221...IAY28 - 18728 - 187
252VALVALASNASN(chain 'IA' and (resid 28 through 220 or (resid 221...IAY195 - 302195 - 302
253ASNASNARGARG(chain 'IA' and (resid 28 through 220 or (resid 221...IAY310 - 435310 - 435
254CYSCYSALAALA(chain 'IA' and (resid 28 through 220 or (resid 221...IAY451 - 528451 - 528
261ALAALAARGARG(chain 'IB' and (resid 28 through 188 or resid 195...IBZ28 - 18728 - 187
262VALVALASNASN(chain 'IB' and (resid 28 through 188 or resid 195...IBZ195 - 302195 - 302
263ASNASNARGARG(chain 'IB' and (resid 28 through 188 or resid 195...IBZ310 - 435310 - 435
264CYSCYSALAALA(chain 'IB' and (resid 28 through 188 or resid 195...IBZ451 - 528451 - 528
271ALAALAARGARG(chain 'IC' and (resid 28 through 188 or resid 195...ICAA28 - 18728 - 187
272VALVALASNASN(chain 'IC' and (resid 28 through 188 or resid 195...ICAA195 - 302195 - 302
273ASNASNARGARG(chain 'IC' and (resid 28 through 188 or resid 195...ICAA310 - 435310 - 435
274CYSCYSALAALA(chain 'IC' and (resid 28 through 188 or resid 195...ICAA451 - 528451 - 528
281ALAALAARGARG(chain 'JA' and (resid 28 through 220 or (resid 221...JABA28 - 18728 - 187
282VALVALASNASN(chain 'JA' and (resid 28 through 220 or (resid 221...JABA195 - 302195 - 302
283ASNASNARGARG(chain 'JA' and (resid 28 through 220 or (resid 221...JABA310 - 435310 - 435
284CYSCYSALAALA(chain 'JA' and (resid 28 through 220 or (resid 221...JABA451 - 528451 - 528
291ALAALAARGARG(chain 'JB' and (resid 28 through 188 or resid 195...JBCA28 - 18728 - 187
292VALVALASNASN(chain 'JB' and (resid 28 through 188 or resid 195...JBCA195 - 302195 - 302
293ASNASNARGARG(chain 'JB' and (resid 28 through 188 or resid 195...JBCA310 - 435310 - 435
294CYSCYSALAALA(chain 'JB' and (resid 28 through 188 or resid 195...JBCA451 - 528451 - 528
301ALAALAARGARG(chain 'JC' and (resid 28 through 188 or resid 195...JCDA28 - 18728 - 187
302VALVALASNASN(chain 'JC' and (resid 28 through 188 or resid 195...JCDA195 - 302195 - 302
303ASNASNARGARG(chain 'JC' and (resid 28 through 188 or resid 195...JCDA310 - 435310 - 435
304CYSCYSALAALA(chain 'JC' and (resid 28 through 188 or resid 195...JCDA451 - 528451 - 528
311ALAALAARGARG(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA28 - 18728 - 187
312VALVALASNASN(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA195 - 302195 - 302
313ASNASNARGARG(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA310 - 435310 - 435
314CYSCYSALAALA(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA451 - 528451 - 528
321ALAALAARGARG(chain 'KB' and (resid 28 through 188 or resid 195...KBFA28 - 18728 - 187
322VALVALASNASN(chain 'KB' and (resid 28 through 188 or resid 195...KBFA195 - 302195 - 302
323ASNASNARGARG(chain 'KB' and (resid 28 through 188 or resid 195...KBFA310 - 435310 - 435
324CYSCYSALAALA(chain 'KB' and (resid 28 through 188 or resid 195...KBFA451 - 528451 - 528
331ALAALAARGARG(chain 'KC' and (resid 28 through 188 or resid 195...KCGA28 - 18728 - 187
332VALVALASNASN(chain 'KC' and (resid 28 through 188 or resid 195...KCGA195 - 302195 - 302
333ASNASNARGARG(chain 'KC' and (resid 28 through 188 or resid 195...KCGA310 - 435310 - 435
334CYSCYSALAALA(chain 'KC' and (resid 28 through 188 or resid 195...KCGA451 - 528451 - 528
341ALAALAARGARG(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA28 - 18728 - 187
342VALVALASNASN(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA195 - 302195 - 302
343ASNASNARGARG(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA310 - 435310 - 435
344CYSCYSALAALA(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA451 - 528451 - 528
351ALAALAARGARG(chain 'LB' and (resid 28 through 188 or resid 195...LBIA28 - 18728 - 187
352VALVALASNASN(chain 'LB' and (resid 28 through 188 or resid 195...LBIA195 - 302195 - 302
353ASNASNARGARG(chain 'LB' and (resid 28 through 188 or resid 195...LBIA310 - 435310 - 435
354CYSCYSALAALA(chain 'LB' and (resid 28 through 188 or resid 195...LBIA451 - 528451 - 528
361ALAALAARGARG(chain 'LC' and (resid 28 through 188 or resid 195...LCJA28 - 18728 - 187
362VALVALASNASN(chain 'LC' and (resid 28 through 188 or resid 195...LCJA195 - 302195 - 302
363ASNASNARGARG(chain 'LC' and (resid 28 through 188 or resid 195...LCJA310 - 435310 - 435
364CYSCYSALAALA(chain 'LC' and (resid 28 through 188 or resid 195...LCJA451 - 528451 - 528
371ALAALAARGARG(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA28 - 18728 - 187
372VALVALASNASN(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA195 - 302195 - 302
373ASNASNARGARG(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA310 - 435310 - 435
374CYSCYSALAALA(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA451 - 528451 - 528
381ALAALAARGARG(chain 'MB' and (resid 28 through 188 or resid 195...MBLA28 - 18728 - 187
382VALVALASNASN(chain 'MB' and (resid 28 through 188 or resid 195...MBLA195 - 302195 - 302
383ASNASNARGARG(chain 'MB' and (resid 28 through 188 or resid 195...MBLA310 - 435310 - 435
384CYSCYSALAALA(chain 'MB' and (resid 28 through 188 or resid 195...MBLA451 - 528451 - 528
391ALAALAARGARG(chain 'MC' and (resid 28 through 188 or resid 195...MCMA28 - 18728 - 187
392VALVALASNASN(chain 'MC' and (resid 28 through 188 or resid 195...MCMA195 - 302195 - 302
393ASNASNARGARG(chain 'MC' and (resid 28 through 188 or resid 195...MCMA310 - 435310 - 435
394CYSCYSALAALA(chain 'MC' and (resid 28 through 188 or resid 195...MCMA451 - 528451 - 528
401ALAALAARGARG(chain 'NA' and (resid 28 through 220 or (resid 221...NANA28 - 18728 - 187
402VALVALASNASN(chain 'NA' and (resid 28 through 220 or (resid 221...NANA195 - 302195 - 302
403ASNASNARGARG(chain 'NA' and (resid 28 through 220 or (resid 221...NANA310 - 435310 - 435
404CYSCYSALAALA(chain 'NA' and (resid 28 through 220 or (resid 221...NANA451 - 528451 - 528
411ALAALAARGARG(chain 'NB' and (resid 28 through 188 or resid 195...NBOA28 - 18728 - 187
412VALVALASNASN(chain 'NB' and (resid 28 through 188 or resid 195...NBOA195 - 302195 - 302
413ASNASNARGARG(chain 'NB' and (resid 28 through 188 or resid 195...NBOA310 - 435310 - 435
414CYSCYSALAALA(chain 'NB' and (resid 28 through 188 or resid 195...NBOA451 - 528451 - 528
421ALAALAARGARG(chain 'NC' and (resid 28 through 188 or resid 195...NCPA28 - 18728 - 187
422VALVALASNASN(chain 'NC' and (resid 28 through 188 or resid 195...NCPA195 - 302195 - 302
423ASNASNARGARG(chain 'NC' and (resid 28 through 188 or resid 195...NCPA310 - 435310 - 435
424CYSCYSALAALA(chain 'NC' and (resid 28 through 188 or resid 195...NCPA451 - 528451 - 528
431ALAALAARGARG(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA28 - 18728 - 187
432VALVALASNASN(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA195 - 302195 - 302
433ASNASNARGARG(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA310 - 435310 - 435
434CYSCYSALAALA(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA451 - 528451 - 528
441ALAALAARGARG(chain 'OB' and (resid 28 through 188 or resid 195...OBRA28 - 18728 - 187
442VALVALASNASN(chain 'OB' and (resid 28 through 188 or resid 195...OBRA195 - 302195 - 302
443ASNASNARGARG(chain 'OB' and (resid 28 through 188 or resid 195...OBRA310 - 435310 - 435
444CYSCYSALAALA(chain 'OB' and (resid 28 through 188 or resid 195...OBRA451 - 528451 - 528
451ALAALAARGARG(chain 'OC' and (resid 28 through 188 or resid 195...OCSA28 - 18728 - 187
452VALVALASNASN(chain 'OC' and (resid 28 through 188 or resid 195...OCSA195 - 302195 - 302
453ASNASNARGARG(chain 'OC' and (resid 28 through 188 or resid 195...OCSA310 - 435310 - 435
454CYSCYSALAALA(chain 'OC' and (resid 28 through 188 or resid 195...OCSA451 - 528451 - 528

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要素

#1: タンパク質 ...
Capsid protein VP1


分子量: 58760.895 Da / 分子数: 45 / 由来タイプ: 組換発現
由来: (組換発現) Norovirus Hu/Houston/TCH186/2002/US (ウイルス)
細胞株 (発現宿主): Sf9
発現宿主: Insect cell expression vector pTIE1 (その他)
参照: UniProt: A9YYE4
#2: 化合物...
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 50 / 由来タイプ: 合成 / 式: Cl
#3: 化合物...
ChemComp-CD / CADMIUM ION


分子量: 112.411 Da / 分子数: 22 / 由来タイプ: 合成 / 式: Cd / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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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: 4.34 Å3/Da / 溶媒含有率: 71.67 %
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: 4.6
詳細: 0.1 M Na Acetate pH 4.6, 0.1 M Cadmium Chloride, 30% PEG 400

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.9794806 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2004年11月29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: 0.9794806 Å / 相対比: 1
反射解像度: 3→30 Å / Num. obs: 841777 / % possible obs: 98.4 % / 冗長度: 3.2 % / Biso Wilson estimate: 67.97 Å2 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.163 / Net I/σ(I): 7
反射 シェル解像度: 3→3.05 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1 / Num. unique obs: 38566 / Rpim(I) all: 0.63 / % possible all: 90.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
HKL-2000データ削減
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
開始モデル: 1ihm

1ihm


解像度: 3→30 Å / SU ML: 0.3942 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 26.4771
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2418 40708 4.97 %
Rwork0.2071 778541 -
obs0.2088 819249 95.75 %
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 mean: 67.79 Å2
精密化ステップサイクル: LAST / 解像度: 3→30 Å
タンパク質核酸リガンド溶媒全体
原子数176443 0 76 3 176522
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0036181805
X-RAY DIFFRACTIONf_angle_d0.7703249531
X-RAY DIFFRACTIONf_chiral_restr0.051927916
X-RAY DIFFRACTIONf_plane_restr0.006433286
X-RAY DIFFRACTIONf_dihedral_angle_d3.8767107203
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.37368890.331217333X-RAY DIFFRACTION64.19
3.03-3.070.362710150.313319647X-RAY DIFFRACTION72.73
3.07-3.110.353310760.296321566X-RAY DIFFRACTION79.91
3.11-3.150.328511420.291922952X-RAY DIFFRACTION84.83
3.15-3.190.338812750.286624172X-RAY DIFFRACTION89.47
3.19-3.230.326612920.282725171X-RAY DIFFRACTION93.12
3.23-3.280.319813190.28825893X-RAY DIFFRACTION96.03
3.28-3.330.332213760.268626339X-RAY DIFFRACTION97.66
3.33-3.380.311913690.2726660X-RAY DIFFRACTION98.54
3.38-3.430.304814110.260526759X-RAY DIFFRACTION98.98
3.43-3.490.291314400.255126803X-RAY DIFFRACTION99.31
3.49-3.560.303414340.25926849X-RAY DIFFRACTION99.5
3.56-3.620.278613820.234826993X-RAY DIFFRACTION99.67
3.62-3.70.275913700.236827003X-RAY DIFFRACTION99.84
3.7-3.780.273714020.225926944X-RAY DIFFRACTION99.89
3.78-3.870.265814950.226526975X-RAY DIFFRACTION99.94
3.87-3.960.249514530.207527068X-RAY DIFFRACTION99.94
3.96-4.070.236413690.208227040X-RAY DIFFRACTION99.95
4.07-4.190.232414310.193727020X-RAY DIFFRACTION99.92
4.19-4.320.215214250.17727113X-RAY DIFFRACTION99.92
4.32-4.480.20713140.17327150X-RAY DIFFRACTION99.89
4.48-4.660.197913500.164827109X-RAY DIFFRACTION99.9
4.66-4.870.186413820.158527189X-RAY DIFFRACTION99.95
4.87-5.120.196414830.163727094X-RAY DIFFRACTION99.98
5.12-5.440.20814840.171327082X-RAY DIFFRACTION99.99
5.44-5.860.224213740.184227251X-RAY DIFFRACTION99.99
5.86-6.450.232614860.197127197X-RAY DIFFRACTION99.97
6.45-7.370.212413910.186627330X-RAY DIFFRACTION99.82
7.37-9.230.195614960.163727352X-RAY DIFFRACTION99.99
9.23-300.2115830.200127487X-RAY DIFFRACTION99.06

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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://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