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- PDB-5kov: Crystal structure of the human astrovirus 2 capsid protein spike ... -

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基本情報

登録情報
データベース: PDB / ID: 5kov
タイトルCrystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-A resolution
要素
  • Capsid polyprotein VP90
  • PL-2 scFv chain
キーワードVIRAL PROTEIN / capsid protein / icosahedral virus / single chain variable fragment.
機能・相同性
機能・相同性情報


T=3 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host extracellular space
類似検索 - 分子機能
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Capsid polyprotein VP90
類似検索 - 構成要素
生物種Human astrovirus-2 (ウイルス)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.245 Å
データ登録者Bogdanoff, W.A. / DuBois, R.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)AI095369 米国
引用ジャーナル: J. Virol. / 年: 2017
タイトル: Structure of a Human Astrovirus Capsid-Antibody Complex and Mechanistic Insights into Virus Neutralization.
著者: Bogdanoff, W.A. / Campos, J. / Perez, E.I. / Yin, L. / Alexander, D.L. / DuBois, R.M.
履歴
登録2016年7月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年11月9日Provider: repository / タイプ: Initial release
改定 1.12016年11月16日Group: Database references
改定 1.22017年1月18日Group: Database references
改定 1.32017年9月6日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42017年11月1日Group: Author supporting evidence / カテゴリ: pdbx_struct_assembly_auth_evidence
改定 1.52019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.62020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.72023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.82024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Capsid polyprotein VP90
C: PL-2 scFv chain
E: PL-2 scFv chain
B: Capsid polyprotein VP90
H: Capsid polyprotein VP90
K: PL-2 scFv chain
I: PL-2 scFv chain
G: Capsid polyprotein VP90
N: Capsid polyprotein VP90
Q: PL-2 scFv chain
O: PL-2 scFv chain
M: Capsid polyprotein VP90
S: Capsid polyprotein VP90
W: PL-2 scFv chain
U: PL-2 scFv chain
T: Capsid polyprotein VP90
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)422,55720
ポリマ－421,67316
非ポリマー8854
水00
1
A: Capsid polyprotein VP90
C: PL-2 scFv chain
E: PL-2 scFv chain
B: Capsid polyprotein VP90
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)105,8616
ポリマ－105,4184
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
H: Capsid polyprotein VP90
K: PL-2 scFv chain
I: PL-2 scFv chain
G: Capsid polyprotein VP90
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)105,8616
ポリマ－105,4184
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
N: Capsid polyprotein VP90
Q: PL-2 scFv chain
O: PL-2 scFv chain
M: Capsid polyprotein VP90


分子量 (理論値)分子数
合計 (水以外)105,4184
ポリマ－105,4184
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
S: Capsid polyprotein VP90
W: PL-2 scFv chain
U: PL-2 scFv chain
T: Capsid polyprotein VP90


分子量 (理論値)分子数
合計 (水以外)105,4184
ポリマ－105,4184
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)199.998, 199.998, 157.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 430:447 or resseq 449:473 or resseq...
21(chain B and (resseq 430:447 or resseq 449:473 or resseq...
31(chain G and (resseq 430:447 or resseq 449:473 or resseq...
41(chain H and (resseq 430:447 or resseq 449:473 or resseq...
51(chain M and (resseq 430:447 or resseq 449:473 or resseq...
61(chain N and (resseq 430:447 or resseq 449:473 or resseq...
71(chain S and (resseq 430:447 or resseq 449:473 or resseq...
81(chain T and (resseq 430:447 or resseq 449:473 or resseq...
12(chain E and (resseq 10 or resseq 12:15 or resseq...
22(chain C and (resseq 10 or resseq 12:15 or resseq...
32(chain I and (resseq 10 or resseq 12:15 or resseq...
42(chain K and (resseq 10 or resseq 12:15 or resseq...
52(chain O and (resseq 10 or resseq 12:15 or resseq...
62(chain U and (resseq 10 or resseq 12:15 or resseq...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUASPASP(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA430 - 4474 - 21
121GLNGLNASPASP(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA449 - 47323 - 47
131GLYGLYSERSER(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA475 - 49949 - 73
141ASPASPTHRTHR(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA501 - 53175 - 105
151HISHISLYSLYS(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA535 - 598109 - 172
161ASNASNTHRTHR(chain A and (resseq 430:447 or resseq 449:473 or resseq...AA600 - 644174 - 218
211GLUGLUASPASP(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD430 - 4474 - 21
221GLNGLNASPASP(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD449 - 47323 - 47
231GLYGLYSERSER(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD475 - 49949 - 73
241ASPASPTHRTHR(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD501 - 53175 - 105
251HISHISLYSLYS(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD535 - 598109 - 172
261ASNASNTHRTHR(chain B and (resseq 430:447 or resseq 449:473 or resseq...BD600 - 644174 - 218
311GLUGLUASPASP(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH430 - 4474 - 21
321GLNGLNASPASP(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH449 - 47323 - 47
331GLYGLYSERSER(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH475 - 49949 - 73
341ASPASPTHRTHR(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH501 - 53175 - 105
351HISHISLYSLYS(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH535 - 598109 - 172
361ASNASNTHRTHR(chain G and (resseq 430:447 or resseq 449:473 or resseq...GH600 - 644174 - 218
411GLUGLUASPASP(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE430 - 4474 - 21
421GLNGLNASPASP(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE449 - 47323 - 47
431GLYGLYSERSER(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE475 - 49949 - 73
441ASPASPTHRTHR(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE501 - 53175 - 105
451HISHISLYSLYS(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE535 - 598109 - 172
461ASNASNTHRTHR(chain H and (resseq 430:447 or resseq 449:473 or resseq...HE600 - 644174 - 218
511GLUGLUASPASP(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML430 - 4474 - 21
521GLNGLNASPASP(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML449 - 47323 - 47
531GLYGLYSERSER(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML475 - 49949 - 73
541ASPASPTHRTHR(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML501 - 53175 - 105
551HISHISLYSLYS(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML535 - 598109 - 172
561ASNASNTHRTHR(chain M and (resseq 430:447 or resseq 449:473 or resseq...ML600 - 644174 - 218
611GLUGLUASPASP(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI430 - 4474 - 21
621GLNGLNASPASP(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI449 - 47323 - 47
631GLYGLYSERSER(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI475 - 49949 - 73
641ASPASPTHRTHR(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI501 - 53175 - 105
651HISHISLYSLYS(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI535 - 598109 - 172
661ASNASNTHRTHR(chain N and (resseq 430:447 or resseq 449:473 or resseq...NI600 - 644174 - 218
711GLUGLUASPASP(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM430 - 4474 - 21
721GLNGLNASPASP(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM449 - 47323 - 47
731GLYGLYSERSER(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM475 - 49949 - 73
741ASPASPTHRTHR(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM501 - 53175 - 105
751HISHISLYSLYS(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM535 - 598109 - 172
761ASNASNTHRTHR(chain S and (resseq 430:447 or resseq 449:473 or resseq...SM600 - 644174 - 218
811GLUGLUASPASP(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP430 - 4474 - 21
821GLNGLNASPASP(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP449 - 47323 - 47
831GLYGLYSERSER(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP475 - 49949 - 73
841ASPASPTHRTHR(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP501 - 53175 - 105
851HISHISLYSLYS(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP535 - 598109 - 172
861ASNASNTHRTHR(chain T and (resseq 430:447 or resseq 449:473 or resseq...TP600 - 644174 - 218
112GLYGLYGLYGLY(chain E and (resseq 10 or resseq 12:15 or resseq...EC1012
122VALVALSERSER(chain E and (resseq 10 or resseq 12:15 or resseq...EC12 - 1514 - 17
132SERSERPROPRO(chain E and (resseq 10 or resseq 12:15 or resseq...EC17 - 4119 - 43
142GLYGLYPHEPHE(chain E and (resseq 10 or resseq 12:15 or resseq...EC44 - 8046 - 82
152METMETMETMET(chain E and (resseq 10 or resseq 12:15 or resseq...EC8284
162GLYGLYTYRTYR(chain E and (resseq 10 or resseq 12:15 or resseq...EC91 - 9993 - 101
172GLYGLYVALVAL(chain E and (resseq 10 or resseq 12:15 or resseq...EC101 - 113103 - 115
182ASPASPILEILE(chain E and (resseq 10 or resseq 12:15 or resseq...EC1001 - 1002140 - 141
192METMETLEULEU(chain E and (resseq 10 or resseq 12:15 or resseq...EC1004 - 1104143 - 243
1102ILEILEILEILE(chain E and (resseq 10 or resseq 12:15 or resseq...EC1106245
212GLYGLYGLYGLY(chain C and (resseq 10 or resseq 12:15 or resseq...CB1012
222VALVALSERSER(chain C and (resseq 10 or resseq 12:15 or resseq...CB12 - 1514 - 17
232SERSERPROPRO(chain C and (resseq 10 or resseq 12:15 or resseq...CB17 - 4119 - 43
242GLYGLYPHEPHE(chain C and (resseq 10 or resseq 12:15 or resseq...CB44 - 8046 - 82
252METMETMETMET(chain C and (resseq 10 or resseq 12:15 or resseq...CB8284
262GLYGLYTYRTYR(chain C and (resseq 10 or resseq 12:15 or resseq...CB91 - 9993 - 101
272GLYGLYVALVAL(chain C and (resseq 10 or resseq 12:15 or resseq...CB101 - 113103 - 115
282ASPASPILEILE(chain C and (resseq 10 or resseq 12:15 or resseq...CB1001 - 1002140 - 141
292METMETLEULEU(chain C and (resseq 10 or resseq 12:15 or resseq...CB1004 - 1104143 - 243
2102ILEILEILEILE(chain C and (resseq 10 or resseq 12:15 or resseq...CB1106245
312GLYGLYGLYGLY(chain I and (resseq 10 or resseq 12:15 or resseq...IG1012
322VALVALSERSER(chain I and (resseq 10 or resseq 12:15 or resseq...IG12 - 1514 - 17
332SERSERPROPRO(chain I and (resseq 10 or resseq 12:15 or resseq...IG17 - 4119 - 43
342GLYGLYPHEPHE(chain I and (resseq 10 or resseq 12:15 or resseq...IG44 - 8046 - 82
352METMETMETMET(chain I and (resseq 10 or resseq 12:15 or resseq...IG8284
362GLYGLYTYRTYR(chain I and (resseq 10 or resseq 12:15 or resseq...IG91 - 9993 - 101
372GLYGLYVALVAL(chain I and (resseq 10 or resseq 12:15 or resseq...IG101 - 113103 - 115
382ASPASPILEILE(chain I and (resseq 10 or resseq 12:15 or resseq...IG1001 - 1002140 - 141
392METMETLEULEU(chain I and (resseq 10 or resseq 12:15 or resseq...IG1004 - 1104143 - 243
3102ILEILEILEILE(chain I and (resseq 10 or resseq 12:15 or resseq...IG1106245
412GLYGLYGLYGLY(chain K and (resseq 10 or resseq 12:15 or resseq...KF1012
422VALVALSERSER(chain K and (resseq 10 or resseq 12:15 or resseq...KF12 - 1514 - 17
432SERSERPROPRO(chain K and (resseq 10 or resseq 12:15 or resseq...KF17 - 4119 - 43
442GLYGLYPHEPHE(chain K and (resseq 10 or resseq 12:15 or resseq...KF44 - 8046 - 82
452METMETMETMET(chain K and (resseq 10 or resseq 12:15 or resseq...KF8284
462GLYGLYTYRTYR(chain K and (resseq 10 or resseq 12:15 or resseq...KF91 - 9993 - 101
472GLYGLYVALVAL(chain K and (resseq 10 or resseq 12:15 or resseq...KF101 - 113103 - 115
482ASPASPILEILE(chain K and (resseq 10 or resseq 12:15 or resseq...KF1001 - 1002140 - 141
492METMETLEULEU(chain K and (resseq 10 or resseq 12:15 or resseq...KF1004 - 1104143 - 243
4102ILEILEILEILE(chain K and (resseq 10 or resseq 12:15 or resseq...KF1106245
512GLYGLYGLYGLY(chain O and (resseq 10 or resseq 12:15 or resseq...OK1012
522VALVALSERSER(chain O and (resseq 10 or resseq 12:15 or resseq...OK12 - 1514 - 17
532SERSERPROPRO(chain O and (resseq 10 or resseq 12:15 or resseq...OK17 - 4119 - 43
542GLYGLYPHEPHE(chain O and (resseq 10 or resseq 12:15 or resseq...OK44 - 8046 - 82
552METMETMETMET(chain O and (resseq 10 or resseq 12:15 or resseq...OK8284
562GLYGLYTYRTYR(chain O and (resseq 10 or resseq 12:15 or resseq...OK91 - 9993 - 101
572GLYGLYVALVAL(chain O and (resseq 10 or resseq 12:15 or resseq...OK101 - 113103 - 115
582ASPASPILEILE(chain O and (resseq 10 or resseq 12:15 or resseq...OK1001 - 1002140 - 141
592METMETLEULEU(chain O and (resseq 10 or resseq 12:15 or resseq...OK1004 - 1104143 - 243
5102ILEILEILEILE(chain O and (resseq 10 or resseq 12:15 or resseq...OK1106245
612GLYGLYGLYGLY(chain U and (resseq 10 or resseq 12:15 or resseq...UO1012
622VALVALSERSER(chain U and (resseq 10 or resseq 12:15 or resseq...UO12 - 1514 - 17
632SERSERPROPRO(chain U and (resseq 10 or resseq 12:15 or resseq...UO17 - 4119 - 43
642GLYGLYPHEPHE(chain U and (resseq 10 or resseq 12:15 or resseq...UO44 - 8046 - 82
652METMETMETMET(chain U and (resseq 10 or resseq 12:15 or resseq...UO8284
662GLYGLYTYRTYR(chain U and (resseq 10 or resseq 12:15 or resseq...UO91 - 9993 - 101
672GLYGLYVALVAL(chain U and (resseq 10 or resseq 12:15 or resseq...UO101 - 113103 - 115
682ASPASPILEILE(chain U and (resseq 10 or resseq 12:15 or resseq...UO1001 - 1002140 - 141
692METMETLEULEU(chain U and (resseq 10 or resseq 12:15 or resseq...UO1004 - 1104143 - 243
6102ILEILEILEILE(chain U and (resseq 10 or resseq 12:15 or resseq...UO1106245

NCSアンサンブル:
ID
1
2
詳細Tetramer confirmed by gel filtration

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要素

#1: タンパク質
Capsid polyprotein VP90


分子量: 25976.566 Da / 分子数: 8 / 断片: UNP Residues 429-644 / 由来タイプ: 組換発現 / 由来: (組換発現) Human astrovirus-2 (ウイルス) / 遺伝子: ORF2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: Q82446
#2: 抗体
PL-2 scFv chain


分子量: 26732.512 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ)
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
株 (発現宿主): Schneider 2 cells
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.96 Å3/Da / 溶媒含有率: 68.93 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 20% PEG 3350, 0.2M Sodium phosphate monobasic.

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 1.033029 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2015年6月18日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.033029 Å / 相対比: 1
反射解像度: 3.2→50 Å / Num. obs: 86484 / % possible obs: 89.2 % / 冗長度: 3.3 % / Biso Wilson estimate: 82.48 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.092 / Rrim(I) all: 0.185 / Χ2: 7.9 / Net I/av σ(I): 13.31 / Net I/σ(I): 10.6 / Num. measured all: 281483
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.312.50.67476280.6670.4810.8341.72279
3.31-3.452.50.50476780.7220.3680.6282.21279.7
3.45-3.62.40.42478200.8220.310.5282.24481
3.6-3.792.50.37679840.850.2760.4692.31982.7
3.79-4.032.60.27381780.9130.1950.3373.28884.7
4.03-4.342.80.20186180.9460.1350.2435.3889
4.34-4.783.20.17292890.9510.110.2057.49596.2
4.78-5.473.80.17396950.950.1020.2018.38999.8
5.47-6.894.60.1697140.9730.0830.1817.651100
6.89-504.90.1198800.9870.0520.12217.40799.9

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
HKL-2000データ収集
HKL-2000データスケーリング
PHASER6.5.0位相決定
PDB_EXTRACT3.2データ抽出
Coot0.8.2モデル構築
HKL-2000データ削減
精密化構造決定の手法: 分子置換
開始モデル: 5I30 5KOU

5i30

5kou


解像度: 3.245→49.999 Å / SU ML: 0.49 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 31.62 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2876 4179 4.84 %
Rwork0.2411 82206 -
obs0.2433 86385 88.1 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 223.3 Å2 / Biso mean: 105.7419 Å2 / Biso min: 31.5 Å2
精密化ステップサイクル: final / 解像度: 3.245→49.999 Å
タンパク質核酸リガンド溶媒全体
原子数25887 0 56 0 25943
Biso mean--159.66 --
残基数----3263
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00426607
X-RAY DIFFRACTIONf_angle_d0.78636180
X-RAY DIFFRACTIONf_chiral_restr0.053991
X-RAY DIFFRACTIONf_plane_restr0.0054590
X-RAY DIFFRACTIONf_dihedral_angle_d10.12915648
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8004X-RAY DIFFRACTION12.854TORSIONAL
12B8004X-RAY DIFFRACTION12.854TORSIONAL
13G8004X-RAY DIFFRACTION12.854TORSIONAL
14H8004X-RAY DIFFRACTION12.854TORSIONAL
15M8004X-RAY DIFFRACTION12.854TORSIONAL
16N8004X-RAY DIFFRACTION12.854TORSIONAL
17S8004X-RAY DIFFRACTION12.854TORSIONAL
18T8004X-RAY DIFFRACTION12.854TORSIONAL
21E5234X-RAY DIFFRACTION12.854TORSIONAL
22C5234X-RAY DIFFRACTION12.854TORSIONAL
23I5234X-RAY DIFFRACTION12.854TORSIONAL
24K5234X-RAY DIFFRACTION12.854TORSIONAL
25O5234X-RAY DIFFRACTION12.854TORSIONAL
26U5234X-RAY DIFFRACTION12.854TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2446-3.28150.3533690.30371616168552
3.2815-3.32010.31851290.33312451258080
3.3201-3.36060.3347990.32682489258879
3.3606-3.40310.41221240.33192421254579
3.4031-3.44790.4261350.30942459259479
3.4479-3.49510.37591250.29572481260680
3.4951-3.5450.34781210.32473259480
3.545-3.59790.34631270.29432481260881
3.5979-3.65410.3861540.282501265581
3.6541-3.7140.29771390.28522531267082
3.714-3.7780.35431280.28112540266882
3.778-3.84670.35161400.29312582272283
3.8467-3.92070.32511360.27262610274684
3.9207-4.00070.33541060.2662619272585
4.0007-4.08760.28431160.2382643275985
4.0876-4.18270.2611740.22982645281986
4.1827-4.28720.24931460.21312742288889
4.2872-4.40310.26381500.20482810296091
4.4031-4.53250.21361360.19962919305593
4.5325-4.67870.27871550.1942990314596
4.6787-4.84580.21691620.18843035319798
4.8458-5.03970.26891560.19833097325399
5.0397-5.26880.24521780.207830933271100
5.2688-5.54620.27471580.195531023260100
5.5462-5.89320.26871550.217531383293100
5.8932-6.34740.30431510.230931133264100
6.3474-6.98470.28511690.246131143283100
6.9847-7.99180.28961380.242631673305100
7.9918-10.05540.22991400.223331693309100
10.0554-50.00540.30061630.27543175333899
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)
10.0021-0.0038-0.0244-0.01950.02140.0251-0.04360.1004-0.06840.0299-0.2555-0.0658-0.22590.056700.4699-0.06810.03820.56820.00860.5052-77.1333-93.613516.8518
20.0482-0.0519-0.04630.10330.02760.02490.0796-0.1898-0.1097-0.0125-0.0850.038-0.76710.1996-00.5375-0.1791-0.05210.437-0.1280.4667-81.571-86.539926.342
30.0083-0.00910.03010.03220.03030.02010.2567-0.21260.0507-0.0874-0.19540.022-0.1347-0.214900.8059-0.1663-0.02510.06180.09290.4646-83.9473-85.729621.3827
40.14770.0285-0.14390.0966-0.1156-0.00260.1170.1548-0.0273-0.0504-0.20850.1381-0.71390.0625-00.6642-0.6206-0.03910.15740.20980.6012-82.0807-87.518711.9603
50.01850.0182-0.01840.0177-0.01660.01240.07780.13650.0311-0.11890.0309-0.0648-0.060.0112-01.1574-0.40950.08320.77570.04210.618-67.1884-80.4461.7498
6-0.04080.1201-0.04080.0108-0.00550.04910.45320.1892-0.14610.2312-0.11110.0524-0.10950.3849-01.1048-1.20580.0791.4605-0.10140.6932-54.5566-83.68341.1857
70.09850.1419-0.0611-0.15-0.0836-0.1262-0.13410.3721-0.212-0.8072-0.14170.1842-0.84541.01520-4.7813-5.43720.0954-3.02520.09990.46-62.9628-89.5654-0.9166
80.0033-0.0004-0.00260.0012-0.00230.00360.0152-0.011-0.0102-0.03020.025-0.07340.0549-0.065400.9918-0.27690.04361.0029-0.05050.81-54.3164-86.212112.3534
90.0699-0.0005-0.03840.10520.00420.03590.1108-0.0404-0.20670.15670.0034-0.0353-0.0218-0.358400.30850.02630.01540.6564-0.10350.5232-112.9631-101.154628.1706
100.00510.0210.0040.0103-0.02830.017-0.1748-0.1011-0.0495-0.0465-0.2104-0.0266-0.0837-0.1008-00.3713-0.0141-0.03790.6157-0.17630.4577-114.1607-105.679523.6365
110.07710.0106-0.01460.05180.00310.05470.0390.1523-0.1055-0.0690.0194-0.0608-0.1137-0.1733-00.4088-0.08180.00540.445-0.00560.6448-104.4547-113.62299.7554
120.01280.01640.02120.00030.02470.00050.0223-0.0550.11610.07250.06190.11910.0096-0.135600.33390.01-0.08250.5010.07080.462-108.9935-117.060311.6781
130.03970.02960.05270.0318-0.02750.03340.02370.00390.0282-0.1371-0.3677-0.13280.09150.0502-01.6478-0.89790.16771.8341-0.22831.0645-49.4645-77.7177-34.6388
140.01510.0085-0.01960.01710.00390.0082-0.0535-0.169-0.0976-0.16310.0620.0942-0.01040.068300.6346-1.02670.03581.4707-0.25080.8058-53.564-89.6448-34.115
150.04180.0040.01560.0004-0.03020.01950.11320.041-0.11770.18730.07750.0051-0.22880.06-01.3567-0.84370.0161.709-0.05440.7939-52.7108-82.372-35.7048
160.02550.01840.0364-0.0092-0.0408-0.0009-0.0531-0.05580.0387-0.0566-0.0649-0.18840.0152-0.40501.1536-0.3649-0.09010.80670.06830.8652-73.6274-81.2846-34.3032
170.0160.1656-0.0472-0.04380.00890.0846-0.3045-0.0175-0.05050.13980.11040.02370.3609-0.317301.109-0.9490.07361.05760.14840.7488-16.7586-40.0483-28.0597
180.0202-0.004-0.02030.0657-0.02350.01330.1910.0790.14480.17790.2272-0.21230.2722-0.3196-01.8707-0.911-0.04481.14850.15270.8589-12.8913-46.8488-31.2948
19-0.02030.0546-0.09910.0561-0.0316-0.0024-0.2712-0.48840.04170.1395-0.1854-0.22630.5814-0.7540-0.4523-2.75350.5268-1.26810.44040.4177-10.681-35.9908-25.2518
200.01030.0470.01410.0426-0.0658-0.0056-0.0970.0312-0.1331-0.032-0.34310.02180.2724-0.18490-0.0685-1.85460.2295-0.02750.15590.5311-10.9666-35.0984-32.164
21-0.00460.0138-0.03090.021-0.02010.0176-0.05980.02010.00610.05820.0058-0.03760.2126-0.0537-00.6419-0.09520.03570.39020.01510.4764-6.0158-25.346-45.1765
220.0477-0.0014-0.0020.0452-0.05180.0514-0.1394-0.09140.0123-0.08880.1894-0.1770.2066-0.8223-00.5356-0.2777-0.0570.5973-0.00730.5536-12.4491-17.1986-51.4183
230.0273-0.00950.0290.0747-0.00980.04230.03-0.12810.0561-0.24710.19470.0063-0.1623-0.1059-00.3383-0.20520.03910.7871-0.04190.554-15.9697-17.8233-52.2172
240.15260.055-0.02440.081-0.08820.021-0.2902-0.14770.04160.08670.0536-0.0160.1176-0.799700.2593-0.47720.1410.7289-0.12920.5681-11.7843-17.3954-40.3403
250.0231-0.0125-0.01720.06470.06470.0326-0.3033-0.0547-0.1394-0.0298-0.1146-0.00610.17070.021602.1896-0.763-0.18151.61620.09490.9315-20.4106-48.49738.2203
26-0.0280.0464-0.02040.0292-0.0070.00750.06740.0395-0.0546-0.10460.1202-0.05920.3631-0.0038-01.6799-1.5689-0.28310.41230.05770.7774-13.4167-49.9146.1437
270.0699-0.0037-0.00260.01870.02890.02590.1507-0.0756-0.01610.17310.046-0.2054-0.0839-0.362601.1215-0.55360.09041.6229-0.1140.8162-16.872-31.07789.2001
28-0.00950.01270.0103-0.0032-0.00020.0183-0.3691-0.023-0.1886-0.02470.0733-0.0315-0.3316-0.118800.8712-0.43780.01291.5408-0.03550.9378-19.8156-27.47295.4205
290.09150.0328-0.01940.0338-0.00310.03180.10720.0005-0.0009-0.18910.0294-0.082-0.54290.021-00.62790.0414-0.08770.3926-0.03030.58821.079813.1585-56.0316
300.03870.0409-0.0486-0.01730.00170.0023-0.0253-0.0753-0.1489-0.1129-0.0796-0.0432-0.22590.0101-00.56380.0126-0.06810.3956-0.02280.3965.672513.8304-50.9246
310.0638-0.030.00490.05910.01570.0544-0.0745-0.25890.12070.1616-0.043-0.1019-0.0951-0.1915-00.4376-0.0613-0.02440.2765-0.04750.52813.48145.8581-37.7016
320.0052-0.0080.0203-0.02310.0799-0.05270.0974-0.0467-0.0051-0.03790.08390.03260.0372-0.09300.4831-0.00640.02950.3392-0.10690.490216.48125.8765-38.8596
330.0092-0.0378-0.01390.05690.02280.02340.58240.06290.22190.0899-0.76770.1634-0.6128-0.4904-00.5789-1.00490.09440.4279-0.17210.8204-58.3474-77.8501-70.9186
340.01530.02110.00670.008-0.0070.00710.2932-0.16470.05460.03340.1347-0.0001-0.099-0.15200.9728-0.31750.05031.0519-0.04090.7567-58.5482-86.7936-69.491
350.07110.02610.06310.0125-0.01180.07910.516-0.373-0.20540.1912-0.4430.1013-0.2520.5927-00.9946-0.6269-0.0340.73240.04410.8519-47.4614-81.8623-72.4225
360.00080.00560.00010.05270.02730.03030.0512-0.2445-0.02650.2428-0.0179-0.02710.1029-0.188701.0672-0.2346-0.09220.64690.05820.7279-54.519-86.6661-74.5734
370.06180.14370.03920.04730.01360.06060.1358-0.0506-0.22920.1254-0.067-0.2012-0.194-0.196100.4637-0.1922-0.01960.5643-0.11380.6451-55.1888-94.3099-97.4887
380.0186-0.0122-0.00860.0324-0.02250.08150.18460.1476-0.07340.0169-0.03160.0088-0.03660.2704-00.5809-0.16160.00510.6598-0.09170.5836-56.65-88.1015-102.5863
390.00740.03390.02340.0174-0.00520.02380.21210.2617-0.16080.03660.1075-0.1783-0.20420.2206-00.5764-0.1345-0.020.4067-0.14870.6797-46.5489-92.6937-95.3837
400.03760.0127-0.01130.04170.03440.0297-0.0440.17320.02020.08920.2434-0.1259-0.0126-0.124100.6507-0.16340.00410.4493-0.04770.6425-52.1056-87.1022-94.2448
410.01440.0324-0.01840.0274-0.03510.03660.0305-0.07-0.21060.3749-0.5613-0.0873-0.1248-0.323601.414-1.64860.18421.6971-0.03160.7568-40.2826-65.0259-44.3501
420.00130.04850.00330.0056-0.00960.01020.01020.0355-0.1677-0.052-0.31610.1154-0.0761-0.0539-01.7719-1.74540.31291.4205-0.07941.0833-35.6132-63.07-49.1627
430.01130.0258-0.0182-0.0080.0410.0110.35720.1027-0.0612-0.1728-0.16410.04820.09620.0617-01.5848-0.6751-0.10751.33330.11350.9432-21.4514-68.2054-60.1542
440.04390.05180.03730.0031-0.0080.03870.164-0.0998-0.0060.18540.08950.22920.13970.036501.3272-1.0027-0.14691.40910.17280.7942-25.0277-62.3057-61.5558
45-0.00190.0008-0.0065-0.00290.00590.0071-0.042-0.0616-0.2106-0.02970.05730.17620.13370.017801.31870.02470.30571.507-0.48331.3072-40.6519-111.4997-118.4558
46-0.00290.0011-0.00950.00770.02010.00650.0259-0.05410.08580.08940.0524-0.1291-0.05760.0727-01.2234-0.31580.25681.658-0.42081.5616-37.4349-104.2532-123.3277
470.0142-0.05340.00220.01740.02080.00430.0145-0.10740.0871-0.1043-0.0542-0.07670.00510.035301.14490.0719-0.00171.4134-0.5331.9848-31.3446-108.8695-110.9363
480.0026-0.0139-0.00370.00110.00270.0010.24030.00670.0059-0.04850.20250.01610.02930.085101.32780.2915-0.26081.1945-0.0881.5868-31.9021-111.8881-98.7298
490.01620.00020.00130.0025-0.0133-0.00240.1898-0.0228-0.0483-0.05930.2649-0.06690.0766-0.0875-00.6166-0.2212-0.0530.6361-0.04350.7256-3.9258-42.1793-95.8111
500.10470.0611-0.06990.05560.09890.0876-0.04620.0644-0.09490.20380.1314-0.19980.0777-0.422500.6635-0.2813-0.17290.41120.03590.6111-8.1449-44.322-84.0092
510.0120.004-0.01-0.0203-0.00320.0178-0.0056-0.03710.01020.17690.1904-0.24320.1069-0.0579-00.7846-0.0609-0.1050.7708-0.04830.9531-5.92-58.9964-93.8349
520.04930.03670.02670.00030.06250.04080.1325-0.004-0.02730.07830.06910.074-0.0454-0.3305-00.5293-0.181-0.08570.4773-0.08810.6298-13.0166-47.4977-88.9999
530.1092-0.0573-0.00060.0281-0.03370.0509-0.75770.25070.2033-0.02830.38430.1006-0.526-0.43200.7258-0.5639-0.09990.93630.10080.7724-21.4463-41.068-114.9042
540.0018-0.00130.00090.0040.00740.0055-0.0452-0.0360.0512-0.0143-0.02830.0089-0.0135-0.02430.00011.10610.15620.00760.9977-0.29321.31111.9288-51.8396-113.7412
550.00440.0404-0.00320.02690.13070.1119-0.47440.18950.0876-0.18840.71280.00420.2658-0.1779-00.7102-0.543-0.03810.9709-0.03090.7541-19.0978-51.3829-112.4924
560.041-0.01420.05220.0112-0.05390.0567-0.16890.0686-0.1304-0.0930.2259-0.1558-0.09830.055700.741-0.34750.04980.9087-0.1020.7219-11.7439-45.5392-112.0509
570.02160.0536-0.01750.0448-0.02280.0419-0.47310.3721-0.00720.00960.0108-0.1748-0.4222-0.3048-01.46-1.5523-0.1151.33940.09410.7595-35.0428-60.297-141.1683
580.05510.00310.00420.0375-0.0240.01880.0246-0.0550.1063-0.17370.0343-0.22750.10160.090801.6488-1.2893-0.07661.8261-0.15771.0105-35.4621-65.5858-138.2927
59-0.00610.11990.00710.003-0.0460.0134-0.1552-0.083-0.01960.19960.6794-0.06910.14720.0501.1834-0.90480.07431.3793-0.11360.8532-34.6501-75.4368-123.8726
60-0.01680.0430.0152-0.00150.01340.0283-0.07470.08080.1253-0.06230.0391-0.0875-0.01410.149101.5264-0.78860.21041.4234-0.17971.0779-38.1849-77.742-127.2353
610.00690.00370.0062-0.0018-0.0039-0.0011-0.07670.06130.0566-0.0169-0.01230.0107-0.03290.0437-01.1239-0.2933-0.46961.65080.33161.665417.0843-62.7081-61.8363
620.0035-0.0092-0.0164-0.00140.00520.0095-0.1828-0.07940.04340.0101-0.1368-0.11960.0643-0.090701.5371-0.0218-0.19771.0150.1391.46447.2599-60.8383-69.0168
630.0234-0.0194-0.03740.0202-0.00530.01120.16990.0561-0.44880.12110.0411-0.0245-0.0048-0.049901.66810.0422-0.27910.97110.04181.76747.3078-66.8618-71.784
640.0004-0.0085-0.0018-0.0018-0.0009-0.00740.13740.0395-0.0538-0.11570.0476-0.050.0920.0115-01.25120.2055-0.21021.3321-0.30521.67226.0745-70.5974-80.9948
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 429:456)A429 - 456
2X-RAY DIFFRACTION2(chain A and resid 457:512)A457 - 512
3X-RAY DIFFRACTION3(chain A and resid 513:554)A513 - 554
4X-RAY DIFFRACTION4(chain A and resid 555:644)A555 - 644
5X-RAY DIFFRACTION5(chain B and resid 430:454)B430 - 454
6X-RAY DIFFRACTION6(chain B and resid 455:507)B455 - 507
7X-RAY DIFFRACTION7(chain B and resid 508:637)B508 - 637
8X-RAY DIFFRACTION8(chain B and resid 638:647)B638 - 647
9X-RAY DIFFRACTION9(chain C and resid 1:81)C1 - 81
10X-RAY DIFFRACTION10(chain C and resid 82:115)C82 - 115
11X-RAY DIFFRACTION11(chain C and resid 1001:1073)C1001 - 1073
12X-RAY DIFFRACTION12(chain C and resid 1074:1108)C1074 - 1108
13X-RAY DIFFRACTION13(chain E and resid 1:35)E1 - 35
14X-RAY DIFFRACTION14(chain E and resid 36:69)E36 - 69
15X-RAY DIFFRACTION15(chain E and resid 70:1001)E70 - 1001
16X-RAY DIFFRACTION16(chain E and resid 1002:1107)E1002 - 1107
17X-RAY DIFFRACTION17(chain G and resid 429:497)G429 - 497
18X-RAY DIFFRACTION18(chain G and resid 498:534)G498 - 534
19X-RAY DIFFRACTION19(chain G and resid 535:609)G535 - 609
20X-RAY DIFFRACTION20(chain G and resid 610:647)G610 - 647
21X-RAY DIFFRACTION21(chain H and resid 429:452)H429 - 452
22X-RAY DIFFRACTION22(chain H and resid 453:499)H453 - 499
23X-RAY DIFFRACTION23(chain H and resid 500:549)H500 - 549
24X-RAY DIFFRACTION24(chain H and resid 550:644)H550 - 644
25X-RAY DIFFRACTION25(chain I and resid 1:44)I1 - 44
26X-RAY DIFFRACTION26(chain I and resid 45:98)I45 - 98
27X-RAY DIFFRACTION27(chain I and resid 99:1026)I99 - 1026
28X-RAY DIFFRACTION28(chain I and resid 1027:1108)I1027 - 1108
29X-RAY DIFFRACTION29(chain K and resid 1:82)K1 - 82
30X-RAY DIFFRACTION30(chain K and resid 83:1001)K83 - 1001
31X-RAY DIFFRACTION31(chain K and resid 1002:1054)K1002 - 1054
32X-RAY DIFFRACTION32(chain K and resid 1055:1108)K1055 - 1108
33X-RAY DIFFRACTION33(chain M and resid 429:514)M429 - 514
34X-RAY DIFFRACTION34(chain M and resid 515:544)M515 - 544
35X-RAY DIFFRACTION35(chain M and resid 545:603)M545 - 603
36X-RAY DIFFRACTION36(chain M and resid 604:644)M604 - 644
37X-RAY DIFFRACTION37(chain N and resid 429:499)N429 - 499
38X-RAY DIFFRACTION38(chain N and resid 500:541)N500 - 541
39X-RAY DIFFRACTION39(chain N and resid 542:604)N542 - 604
40X-RAY DIFFRACTION40(chain N and resid 605:645)N605 - 645
41X-RAY DIFFRACTION41(chain O and resid 1:80)O1 - 80
42X-RAY DIFFRACTION42(chain O and resid 81:114)O81 - 114
43X-RAY DIFFRACTION43(chain O and resid 115:1038)O115 - 1038
44X-RAY DIFFRACTION44(chain O and resid 1039:1108)O1039 - 1108
45X-RAY DIFFRACTION45(chain Q and resid 19:51)Q19 - 51
46X-RAY DIFFRACTION46(chain Q and resid 52:78)Q52 - 78
47X-RAY DIFFRACTION47(chain Q and resid 79:1028)Q79 - 1028
48X-RAY DIFFRACTION48(chain Q and resid 1029:1060)Q1029 - 1060
49X-RAY DIFFRACTION49(chain S and resid 429:448)S429 - 448
50X-RAY DIFFRACTION50(chain S and resid 449:548)S449 - 548
51X-RAY DIFFRACTION51(chain S and resid 549:585)S549 - 585
52X-RAY DIFFRACTION52(chain S and resid 586:646)S586 - 646
53X-RAY DIFFRACTION53(chain T and resid 429:529)T429 - 529
54X-RAY DIFFRACTION54(chain T and resid 530:534)T530 - 534
55X-RAY DIFFRACTION55(chain T and resid 535:598)T535 - 598
56X-RAY DIFFRACTION56(chain T and resid 599:644)T599 - 644
57X-RAY DIFFRACTION57(chain U and resid 1:80)U1 - 80
58X-RAY DIFFRACTION58(chain U and resid 81:110)U81 - 110
59X-RAY DIFFRACTION59(chain U and resid 111:1075)U111 - 1075
60X-RAY DIFFRACTION60(chain U and resid 1076:1108)U1076 - 1108
61X-RAY DIFFRACTION61(chain W and resid 5:25)W5 - 25
62X-RAY DIFFRACTION62(chain W and resid 26:55)W26 - 55
63X-RAY DIFFRACTION63(chain W and resid 56:1051)W56 - 1051
64X-RAY DIFFRACTION64(chain W and resid 1052:1097)W1052 - 1097

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る