PDB-5kwl: expanded poliovirus in complex with VHH 10E

基本情報

• 登録情報: データベース: PDB / ID: 5kwl
• タイトル: expanded poliovirus in complex with VHH 10E

要素

• VHH 10E
• VP1
• VP2
• VP3

• キーワード: VIRUS/Immune System / poliovirus (ポリオウイルス) / VHH / nanobody (ナノボディ) / 80S / expanded / single domain antibody (ナノボディ) / VIRUS-Immune System complex

機能・相同性

分子機能:

symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ピコルナイン2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA依存性RNAポリメラーゼ / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / タンパク質分解 / RNA binding / ATP binding / 生体膜 / metal ion binding

ドメイン・相同性:

Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / ヘリカーゼ / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase

構成要素:

Genome polyprotein

• 生物種: Camelus dromedarius (ヒトコブラクダ); Poliovirus type 1 (ポリオウイルス)
• 手法: 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.8 Å
• データ登録者: Strauss, M. / Schotte, L. / Filman, D.J. / Hogle, J.M.

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)	AI020566	米国

• 引用: ジャーナル: J Virol / 年: 2017; タイトル: Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.; 著者: Mike Strauss / Lise Schotte / Krishanthi S Karunatilaka / David J Filman / James M Hogle / ; 要旨: By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion.; IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events.

履歴

登録	2016年7月18日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2016年11月2日	Provider: repository / タイプ: Initial release
改定 1.1	2016年11月9日	Group: Other
改定 1.2	2016年11月30日	Group: Database references
改定 1.3	2017年2月1日	Group: Database references / Other
改定 1.4	2017年2月8日	Group: Database references
改定 1.5	2017年9月27日	Group: Author supporting evidence / Data collection / カテゴリ: em_software / pdbx_audit_support Item: _em_software.name / _pdbx_audit_support.funding_organization
改定 1.6	2018年7月18日	Group: Data collection / カテゴリ: em_software / Item: _em_software.name
改定 1.7	2019年12月11日	Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.8	2019年12月18日	Group: Other / カテゴリ: atom_sites / cell Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c

集合体

登録構造単位

1: VP1

2: VP2

3: VP3

7: VHH 10E

概要:

• 92.1 kDa, 4 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	92,127	4
ポリマ－	92,127	4
非ポリマー	0	0
水	0

1

1: VP1

2: VP2

3: VP3

7: VHH 10E

x 60

概要:

• complete icosahedral assembly
• 5.53 MDa, 240 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	5,527,616	240
ポリマ－	5,527,616	240
非ポリマー	0	0
水	0

対称操作:

タイプ	名称	対称操作	数
point symmetry operation			60

2

概要:

• 登録構造と同一（異なる座標系）
• icosahedral asymmetric unit

対称操作:

タイプ	名称	対称操作	数
point symmetry operation			1

3

1: VP1

2: VP2

3: VP3

7: VHH 10E

x 5

概要:

• icosahedral pentamer
• 461 kDa, 20 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	460,635	20
ポリマ－	460,635	20
非ポリマー	0	0
水	0

対称操作:

タイプ	名称	対称操作	数
point symmetry operation			5

4

1: VP1

2: VP2

3: VP3

7: VHH 10E

x 6

概要:

• icosahedral 23 hexamer
• 553 kDa, 24 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	552,762	24
ポリマ－	552,762	24
非ポリマー	0	0
水	0

対称操作:

タイプ	名称	対称操作	数
point symmetry operation			6

5

概要:

• 登録構造と同一（異なる座標系）
• icosahedral asymmetric unit, std point frame

対称操作:

タイプ	名称	対称操作	数
transform to point frame			1

• 対称性: 点対称性: (シェーンフリース記号: I (正20面体型対称))

非結晶学的対称性 (NCS)

NCSドメイン:

ID	Ens-ID	詳細
1	1	1
2	1	A
3	1	D
4	1	E
5	1	F
6	1	V
7	1	W
8	1	X
1	2	2
2	2	B
3	2	G
4	2	J
5	2	L
6	2	N
1	3	3
2	3	C
3	3	H
4	3	I
5	3	K
6	3	M
7	3	T
8	3	U
1	4	7
2	4	S
1	5	1
2	5	A
3	5	D
4	5	E
5	5	F
6	5	V
7	5	W
8	5	X
1	6	2
2	6	B
3	6	G
4	6	J
5	6	L
6	6	N
1	7	3
2	7	C
3	7	H
4	7	I
5	7	K
6	7	M
7	7	T
8	7	U
1	8	7
2	8	S
1	9	1
2	9	A
3	9	D
4	9	E
5	9	F
6	9	V
7	9	W
8	9	X
1	10	2
2	10	B
3	10	G
4	10	J
5	10	L
6	10	N
1	11	3
2	11	C
3	11	H
4	11	I
5	11	K
6	11	M
7	11	T
8	11	U
1	12	7
2	12	S

NCSドメイン領域:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	1	57 - 213
2	1	1	1	A	57 - 213
3	1	1	1	D	57 - 213
4	1	1	1	E	57 - 213
5	1	1	1	F	57 - 213
6	1	1	1	V	57 - 213
7	1	1	1	W	57 - 213
8	1	1	1	X	57 - 213
1	2	1	1	1	232 - 279
2	2	1	1	A	232 - 279
3	2	1	1	D	232 - 279
4	2	1	1	E	232 - 279
5	2	1	1	F	232 - 279
6	2	1	1	V	232 - 279
7	2	1	1	W	232 - 279
8	2	1	1	X	232 - 279
1	1	2	1	2	1 - 43
2	1	2	1	B	1 - 43
3	1	2	1	G	1 - 43
4	1	2	1	J	1 - 43
5	1	2	1	L	1 - 43
6	1	2	1	N	1 - 43
1	2	2	1	2	53 - 159
2	2	2	1	B	53 - 159
3	2	2	1	G	53 - 159
4	2	2	1	J	53 - 159
5	2	2	1	L	53 - 159
6	2	2	1	N	53 - 159
1	3	2	1	2	174 - 269
2	3	2	1	B	174 - 269
3	3	2	1	G	174 - 269
4	3	2	1	J	174 - 269
5	3	2	1	L	174 - 269
6	3	2	1	N	174 - 269
1	1	3	1	3	1 - 231
2	1	3	1	C	1 - 231
3	1	3	1	H	1 - 231
4	1	3	1	I	1 - 231
5	1	3	1	K	1 - 231
6	1	3	1	M	1 - 231
7	1	3	1	T	1 - 231
8	1	3	1	U	1 - 231
1	1	4	1	7	1 - 124
2	1	4	1	S	1 - 124
1	1	5	1	1	65 - 212
2	1	5	1	A	65 - 212
3	1	5	1	D	65 - 212
4	1	5	1	E	65 - 212
5	1	5	1	F	65 - 212
6	1	5	1	V	65 - 212
7	1	5	1	W	65 - 212
8	1	5	1	X	65 - 212
1	2	5	1	1	232 - 279
2	2	5	1	A	232 - 279
3	2	5	1	D	232 - 279
4	2	5	1	E	232 - 279
5	2	5	1	F	232 - 279
6	2	5	1	V	232 - 279
7	2	5	1	W	232 - 279
8	2	5	1	X	232 - 279
1	1	6	1	2	1 - 43
2	1	6	1	B	1 - 43
3	1	6	1	G	1 - 43
4	1	6	1	J	1 - 43
5	1	6	1	L	1 - 43
6	1	6	1	N	1 - 43
1	2	6	1	2	55 - 133
2	2	6	1	B	55 - 133
3	2	6	1	G	55 - 133
4	2	6	1	J	55 - 133
5	2	6	1	L	55 - 133
6	2	6	1	N	55 - 133
1	3	6	1	2	140 - 159
2	3	6	1	B	140 - 159
3	3	6	1	G	140 - 159
4	3	6	1	J	140 - 159
5	3	6	1	L	140 - 159
6	3	6	1	N	140 - 159
1	4	6	1	2	175 - 272
2	4	6	1	B	175 - 272
3	4	6	1	G	175 - 272
4	4	6	1	J	175 - 272
5	4	6	1	L	175 - 272
6	4	6	1	N	175 - 272
1	1	7	1	3	1 - 230
2	1	7	1	C	1 - 230
3	1	7	1	H	1 - 230
4	1	7	1	I	1 - 230
5	1	7	1	K	1 - 230
6	1	7	1	M	1 - 230
7	1	7	1	T	1 - 230
8	1	7	1	U	1 - 230
1	1	8	1	7	1 - 124
2	1	8	1	S	1 - 124
1	1	9	1	1	71 - 212
2	1	9	1	A	71 - 212
3	1	9	1	D	71 - 212
4	1	9	1	E	71 - 212
5	1	9	1	F	71 - 212
6	1	9	1	V	71 - 212
7	1	9	1	W	71 - 212
8	1	9	1	X	71 - 212
1	2	9	1	1	232 - 279
2	2	9	1	A	232 - 279
3	2	9	1	D	232 - 279
4	2	9	1	E	232 - 279
5	2	9	1	F	232 - 279
6	2	9	1	V	232 - 279
7	2	9	1	W	232 - 279
8	2	9	1	X	232 - 279
1	1	10	1	2	1 - 42
2	1	10	1	B	1 - 42
3	1	10	1	G	1 - 42
4	1	10	1	J	1 - 42
5	1	10	1	L	1 - 42
6	1	10	1	N	1 - 42
1	2	10	1	2	55 - 159
2	2	10	1	B	55 - 159
3	2	10	1	G	55 - 159
4	2	10	1	J	55 - 159
5	2	10	1	L	55 - 159
6	2	10	1	N	55 - 159
1	3	10	1	2	175 - 268
2	3	10	1	B	175 - 268
3	3	10	1	G	175 - 268
4	3	10	1	J	175 - 268
5	3	10	1	L	175 - 268
6	3	10	1	N	175 - 268
1	1	11	1	3	1 - 230
2	1	11	1	C	1 - 230
3	1	11	1	H	1 - 230
4	1	11	1	I	1 - 230
5	1	11	1	K	1 - 230
6	1	11	1	M	1 - 230
7	1	11	1	T	1 - 230
8	1	11	1	U	1 - 230
1	1	12	1	7	1 - 124
2	1	12	1	S	1 - 124

NCSアンサンブル:

ID
1
2
3
4
5
6
7
8
9
10
11
12

NCS oper:

ID	Code	Matrix	ベクター
1	given	(1), (1), (1)
2	given	(0.308947, 0.809174, -0.499789), (-0.809122, 0.499811, 0.309048), (0.499874, 0.308911, 0.809136)	-0.05154, 0.01791, -0.00045
3	given	(-0.80873, 0.500307, -0.309271), (-0.500433, -0.30899, 0.808759), (0.309066, 0.808838, 0.50026)	-0.00914, 0.03233, -0.02408
4	given	(-0.80905, -0.499954, 0.309005), (0.499923, -0.308921, 0.809101), (-0.309055, 0.809082, 0.499871)	-0.00052, -0.00904, -0.00661
5	given	(0.3094, -0.809369, 0.499192), (0.809318, 0.499743, 0.308645), (-0.499275, 0.308511, 0.809658)	0.12889, 0.06892, -0.05558
6	given	(-0.999999, 0.000787, 0.00123), (-0.000787, -1, 0.000644), (0.001231, 0.000643, 0.999999)	-0.11564, -0.11264, 0.05872
7	given	(-0.308665, 0.809433, 0.499544), (-0.809159, -0.49952, 0.309421), (0.499988, -0.308703, 0.809145)	0.08254, -0.02893, -0.00391
8	given	(-0.308718, -0.808202, 0.5015), (0.809535, -0.500066, -0.30755), (0.499346, 0.311036, 0.808647)	-0.1812, -0.17441, 0.14015
9	given	(1), (1), (1)
10	given	(0.309796, 0.808693, -0.500042), (-0.808811, 0.500624, 0.308544), (0.499851, 0.308853, 0.809172)	-0.01852, -0.03142, 0.01647
11	given	(0.30849, -0.809106, 0.500182), (0.809023, 0.49974, 0.309421), (-0.500315, 0.309205, 0.80875)	-0.04023, -0.03907, 0.03686
12	given	(-0.308865, 0.809192, 0.499811), (-0.809079, -0.499795, 0.309186), (0.499994, -0.30889, 0.809069)	0.02191, -0.02136, -0.00739
13	given	(-0.309311, -0.808773, 0.500213), (0.80918, -0.500162, -0.308327), (0.499555, 0.309394, 0.809148)	-0.01033, -0.09286, 0.03359
14	given	(-0.499825, 0.308647, 0.809266), (0.309273, -0.809154, 0.49962), (0.809027, 0.500006, 0.308979)	-0.02726, 0.03577, 0.02027
15	given	(1), (1), (1)
16	given	(0.308995, 0.808931, -0.500153), (-0.808837, 0.500156, 0.309236), (0.500305, 0.30899, 0.808839)	0.00324, -0.04093, 0.01727
17	given	(0.309198, -0.808729, 0.500354), (0.808919, 0.500308, 0.308776), (-0.500047, 0.309273, 0.80889)	-0.04711, 0.00924, 0.01115
18	given	(-1, 0.000124, -6.4E-5), (-0.000125, -1, 0.000423), (-6.4E-5, 0.000423, 1)	0.00195, -0.06586, 0.01564
19	given	(-0.30896, 0.80865, 0.500628), (-0.808993, -0.50022, 0.308723), (0.500073, -0.309622, 0.80874)	-0.09558, 0.0211, 0.02025
20	given	(-0.308695, -0.808937, 0.500329), (0.808875, -0.500014, -0.309366), (0.500429, 0.309204, 0.80868)	-0.07535, 0.05127, 0.01461
21	given	(-0.808942, 0.500052, -0.30913), (-0.500145, -0.309015, 0.808928), (0.30898, 0.808986, 0.500074)	-0.00478, 0.01621, 0.00163
22	given	(-0.808987, -0.500284, 0.308635), (0.499923, -0.309356, 0.808935), (-0.309219, 0.808712, 0.500368)	0.0676, 0.03751, -0.01401
23	given	(1), (1), (1)
24	given	(0.311201, 0.808089, -0.500147), (-0.809773, 0.500934, 0.305505), (0.497415, 0.309932, 0.810259)	-0.08093, 0.36696, -0.02947
25	given	(1), (1), (1)
26	given	(0.308947, 0.809174, -0.499789), (-0.809122, 0.499811, 0.309048), (0.499874, 0.308911, 0.809136)	-0.05154, 0.01791, -0.00045
27	given	(-0.80873, 0.500307, -0.309271), (-0.500433, -0.30899, 0.808759), (0.309066, 0.808838, 0.50026)	-0.00914, 0.03233, -0.02408
28	given	(-0.80905, -0.499954, 0.309005), (0.499923, -0.308921, 0.809101), (-0.309055, 0.809082, 0.499871)	-0.00052, -0.00904, -0.00661
29	given	(0.3094, -0.809369, 0.499192), (0.809318, 0.499743, 0.308645), (-0.499275, 0.308511, 0.809658)	0.12889, 0.06892, -0.05558
30	given	(-0.999999, 0.000787, 0.00123), (-0.000787, -1, 0.000644), (0.001231, 0.000643, 0.999999)	-0.11564, -0.11264, 0.05872
31	given	(-0.308665, 0.809433, 0.499544), (-0.809159, -0.49952, 0.309421), (0.499988, -0.308703, 0.809145)	0.08254, -0.02893, -0.00391
32	given	(-0.308718, -0.808202, 0.5015), (0.809535, -0.500066, -0.30755), (0.499346, 0.311036, 0.808647)	-0.1812, -0.17441, 0.14015
33	given	(1), (1), (1)
34	given	(0.309797, 0.808693, -0.500041), (-0.808812, 0.500624, 0.308542), (0.499848, 0.308855, 0.809173)	-0.01862, -0.03098, 0.01651
35	given	(0.308491, -0.809106, 0.500181), (0.809022, 0.499741, 0.309422), (-0.500316, 0.309204, 0.80875)	-0.04018, -0.0391, 0.03692
36	given	(-0.308866, 0.80919, 0.499813), (-0.809078, -0.499798, 0.309185), (0.499995, -0.308891, 0.809068)	0.02161, -0.02114, -0.00721
37	given	(-0.309312, -0.808773, 0.500212), (0.80918, -0.500162, -0.308327), (0.499554, 0.309393, 0.809149)	-0.01019, -0.09283, 0.03359
38	given	(-0.499834, 0.308648, 0.80926), (0.309272, -0.809151, 0.499626), (0.809022, 0.500012, 0.308985)	-0.0261, 0.03522, 0.01993
39	given	(1), (1), (1)
40	given	(0.308995, 0.808931, -0.500153), (-0.808837, 0.500156, 0.309236), (0.500305, 0.30899, 0.808839)	0.00324, -0.04093, 0.01727
41	given	(0.309198, -0.808729, 0.500354), (0.808919, 0.500308, 0.308776), (-0.500047, 0.309273, 0.80889)	-0.04711, 0.00924, 0.01115
42	given	(-1, 0.000124, -6.4E-5), (-0.000125, -1, 0.000423), (-6.4E-5, 0.000423, 1)	0.00195, -0.06586, 0.01564
43	given	(-0.30896, 0.80865, 0.500628), (-0.808993, -0.50022, 0.308723), (0.500073, -0.309622, 0.80874)	-0.09558, 0.0211, 0.02025
44	given	(-0.308695, -0.808937, 0.500329), (0.808875, -0.500014, -0.309366), (0.500429, 0.309204, 0.80868)	-0.07535, 0.05127, 0.01461
45	given	(-0.808942, 0.500052, -0.30913), (-0.500145, -0.309015, 0.808928), (0.30898, 0.808986, 0.500074)	-0.00478, 0.01621, 0.00163
46	given	(-0.808987, -0.500284, 0.308635), (0.499923, -0.309356, 0.808935), (-0.309219, 0.808712, 0.500368)	0.0676, 0.03751, -0.01401
47	given	(1), (1), (1)
48	given	(0.311201, 0.808089, -0.500147), (-0.809773, 0.500934, 0.305505), (0.497415, 0.309932, 0.810259)	-0.08093, 0.36696, -0.02947
49	given	(1), (1), (1)
50	given	(0.308947, 0.809174, -0.499789), (-0.809122, 0.499811, 0.309048), (0.499874, 0.308911, 0.809136)	-0.05154, 0.01791, -0.00045
51	given	(-0.80873, 0.500307, -0.309271), (-0.500433, -0.30899, 0.808759), (0.309066, 0.808838, 0.50026)	-0.00914, 0.03233, -0.02408
52	given	(-0.80905, -0.499954, 0.309005), (0.499923, -0.308921, 0.809101), (-0.309055, 0.809082, 0.499871)	-0.00052, -0.00904, -0.00661
53	given	(0.3094, -0.809369, 0.499192), (0.809318, 0.499743, 0.308645), (-0.499275, 0.308511, 0.809658)	0.12889, 0.06892, -0.05558
54	given	(-0.999999, 0.000787, 0.00123), (-0.000787, -1, 0.000644), (0.001231, 0.000643, 0.999999)	-0.11564, -0.11264, 0.05872
55	given	(-0.308665, 0.809433, 0.499544), (-0.809159, -0.49952, 0.309421), (0.499988, -0.308703, 0.809145)	0.08254, -0.02893, -0.00391
56	given	(-0.308718, -0.808202, 0.5015), (0.809535, -0.500066, -0.30755), (0.499346, 0.311036, 0.808647)	-0.1812, -0.17441, 0.14015
57	given	(1), (1), (1)
58	given	(0.309796, 0.808693, -0.500042), (-0.808811, 0.500624, 0.308544), (0.499851, 0.308853, 0.809172)	-0.01852, -0.03142, 0.01647
59	given	(0.30849, -0.809106, 0.500182), (0.809023, 0.49974, 0.309421), (-0.500315, 0.309205, 0.80875)	-0.04023, -0.03907, 0.03686
60	given	(-0.308865, 0.809192, 0.499811), (-0.809079, -0.499795, 0.309186), (0.499994, -0.30889, 0.809069)	0.02191, -0.02136, -0.00739
61	given	(-0.309311, -0.808773, 0.500213), (0.80918, -0.500162, -0.308327), (0.499555, 0.309394, 0.809148)	-0.01033, -0.09286, 0.03359
62	given	(-0.499825, 0.308647, 0.809266), (0.309273, -0.809154, 0.49962), (0.809027, 0.500006, 0.308979)	-0.02726, 0.03577, 0.02027
63	given	(1), (1), (1)
64	given	(0.308995, 0.808931, -0.500153), (-0.808837, 0.500156, 0.309236), (0.500305, 0.30899, 0.808839)	0.00324, -0.04093, 0.01727
65	given	(0.309198, -0.808729, 0.500354), (0.808919, 0.500308, 0.308776), (-0.500047, 0.309273, 0.80889)	-0.04711, 0.00924, 0.01115
66	given	(-1, 0.000124, -6.4E-5), (-0.000125, -1, 0.000423), (-6.4E-5, 0.000423, 1)	0.00195, -0.06586, 0.01564
67	given	(-0.30896, 0.80865, 0.500628), (-0.808993, -0.50022, 0.308723), (0.500073, -0.309622, 0.80874)	-0.09558, 0.0211, 0.02025
68	given	(-0.308695, -0.808937, 0.500329), (0.808875, -0.500014, -0.309366), (0.500429, 0.309204, 0.80868)	-0.07535, 0.05127, 0.01461
69	given	(-0.808942, 0.500052, -0.30913), (-0.500145, -0.309015, 0.808928), (0.30898, 0.808986, 0.500074)	-0.00478, 0.01621, 0.00163
70	given	(-0.808987, -0.500284, 0.308635), (0.499923, -0.309356, 0.808935), (-0.309219, 0.808712, 0.500368)	0.0676, 0.03751, -0.01401
71	given	(1), (1), (1)
72	given	(0.311201, 0.808089, -0.500147), (-0.809773, 0.500934, 0.305505), (0.497415, 0.309932, 0.810259)	-0.08093, 0.36696, -0.02947

要素

#1: タンパク質

1 VP1

詳細:

分子量: 23645.768 Da / 分子数: 1 / 断片: UNP residues 650-858 / 由来タイプ: 天然
由来: (天然) Poliovirus type 1 (strain Mahoney) (ポリオウイルス)
株: Mahoney / 参照: UniProt: P03300

#2: タンパク質

2 VP2

詳細:

分子量: 29580.188 Da / 分子数: 1 / 断片: UNP residues 70-337 / 由来タイプ: 天然
由来: (天然) Poliovirus type 1 (strain Mahoney) (ポリオウイルス)
株: Mahoney / 参照: UniProt: P03300

#3: タンパク質

3 VP3

詳細:

分子量: 25664.455 Da / 分子数: 1 / 断片: UNP residues 342-571 / 由来タイプ: 天然
由来: (天然) Poliovirus type 1 (strain Mahoney) (ポリオウイルス)
株: Mahoney / 参照: UniProt: P03300

#4: 抗体

7 VHH 10E

詳細:

分子量: 13236.518 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Camelus dromedarius (ヒトコブラクダ)
発現宿主: Escherichia coli K-12 (大腸菌)

実験情報

実験

• 実験: 手法: 電子顕微鏡法
• EM実験: 試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

試料調製

• 構成要素: 名称: expanded poliovirus (type 1) in complex with VHH 10E; タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES
• 分子量: 値: 9 MDa / 実験値: NO
• 由来(天然): 生物種: Poliovirus type 1 (strain Mahoney) (ポリオウイルス)
• 緩衝液: pH: 7
• 試料: 濃度: 0.9 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
• 急速凍結: 凍結剤: ETHANE

電子顕微鏡撮影

• 実験機器: モデル: Tecnai Polara / 画像提供: FEI Company
• 顕微鏡: モデル: FEI POLARA 300
• 電子銃: 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
• 電子レンズ: モード: BRIGHT FIELDBright-field microscopy
• 撮影: 電子線照射量: 35 e/Ų / 検出モード: SUPER-RESOLUTION; フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
• 画像スキャン: サンプリングサイズ: 5 µm / 横: 3800 / 縦: 3700

解析

• ソフトウェア: 名称: REFMAC / バージョン: 5.8.0151 / 分類: 精密化

EMソフトウェア

ID	名称	バージョン	カテゴリ
1	e2boxer.py		粒子像選択
4	CTFFIND3		CTF補正
7	Coot		モデルフィッティング
11	RELION	1.3	分類
12	GeFrealign and Frealign	9.09	３次元再構成
13	REFMAC	5	モデル精密化

• CTF補正: タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 3次元再構成: 解像度: 4.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 13938 / 対称性のタイプ: POINT
• 原子モデル構築: プロトコル: OTHER / 空間: RECIPROCAL; 詳細: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with the map. Refinement space: reciprocal, using both Fourier amplitudes and phases.

精密化

解像度: 4.5→98.6 Å / Cor.coef. F_o:F_c: 0.729 / SU B: 135.906 / SU ML: 1.653 / ESU R: 1.303
立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES

	Rfactor	反射数	%反射
Rwork	0.48055	-	-
obs	0.48055	228405	99.94 %

• 溶媒の処理: 溶媒モデル: PARAMETERS FOR MASK CACLULATION

原子変位パラメータ

B_iso mean: 24.844 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.62 Å2	-0.87 Å2	0.51 Å2
2-	-	0.34 Å2	-1.05 Å2
3-	-	-	0.28 Å2

拘束条件

Refine-ID	タイプ	Dev ideal	Dev ideal target	数
ELECTRON MICROSCOPY	r_bond_refined_d	0.01	0.019	40774
ELECTRON MICROSCOPY	r_bond_other_d
ELECTRON MICROSCOPY	r_angle_refined_deg	1.999	1.949	55596
ELECTRON MICROSCOPY	r_angle_other_deg
ELECTRON MICROSCOPY	r_dihedral_angle_1_deg	1.676	5	5010
ELECTRON MICROSCOPY	r_dihedral_angle_2_deg	18.484	23.569	1754
ELECTRON MICROSCOPY	r_dihedral_angle_3_deg	9.299	15	6372
ELECTRON MICROSCOPY	r_dihedral_angle_4_deg	8.256	15	220
ELECTRON MICROSCOPY	r_chiral_restr	0.142	0.2	6194
ELECTRON MICROSCOPY	r_gen_planes_refined	0.004	0.021	31120
ELECTRON MICROSCOPY	r_gen_planes_other
ELECTRON MICROSCOPY	r_nbd_refined
ELECTRON MICROSCOPY	r_nbd_other
ELECTRON MICROSCOPY	r_nbtor_refined
ELECTRON MICROSCOPY	r_nbtor_other
ELECTRON MICROSCOPY	r_xyhbond_nbd_refined
ELECTRON MICROSCOPY	r_xyhbond_nbd_other
ELECTRON MICROSCOPY	r_metal_ion_refined
ELECTRON MICROSCOPY	r_metal_ion_other
ELECTRON MICROSCOPY	r_symmetry_vdw_refined
ELECTRON MICROSCOPY	r_symmetry_vdw_other
ELECTRON MICROSCOPY	r_symmetry_hbond_refined
ELECTRON MICROSCOPY	r_symmetry_hbond_other
ELECTRON MICROSCOPY	r_symmetry_metal_ion_refined
ELECTRON MICROSCOPY	r_symmetry_metal_ion_other
ELECTRON MICROSCOPY	r_mcbond_it
ELECTRON MICROSCOPY	r_mcbond_other
ELECTRON MICROSCOPY	r_mcangle_it
ELECTRON MICROSCOPY	r_mcangle_other
ELECTRON MICROSCOPY	r_scbond_it
ELECTRON MICROSCOPY	r_scbond_other
ELECTRON MICROSCOPY	r_scangle_it
ELECTRON MICROSCOPY	r_scangle_other
ELECTRON MICROSCOPY	r_long_range_B_refined
ELECTRON MICROSCOPY	r_long_range_B_other
ELECTRON MICROSCOPY	r_rigid_bond_restr
ELECTRON MICROSCOPY	r_sphericity_free
ELECTRON MICROSCOPY	r_sphericity_bonded

LS精密化 シェル

解像度: 4.5→4.743 Å / Total num. of bins used: 10

	Rfactor	反射数	%反射
Rwork	0.524	33400	-
Rfree	-	0	-
obs	-	-	99.75 %