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- PDB-4c2m: Structure of RNA polymerase I at 2.8 A resolution -

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基本情報

登録情報
データベース: PDB / ID: 4c2m
タイトルStructure of RNA polymerase I at 2.8 A resolution
要素
  • (DNA-DIRECTED RNA POLYMERASE I SUBUNIT ...) x 7
  • (DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ...) x 2
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...) x 5
キーワードTRANSCRIPTION / RIBOSOME BIOGENESIS
機能・相同性
機能・相同性情報


RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / regulation of cell size / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes ...RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / regulation of cell size / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
類似検索 - 分子機能
Alpha-Beta Plaits - #2850 / Helix Hairpins - #1770 / Tetracycline Repressor; domain 2 - #120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / : / RNA polymerase Rpb1 funnel domain / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 ...Alpha-Beta Plaits - #2850 / Helix Hairpins - #1770 / Tetracycline Repressor; domain 2 - #120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / : / RNA polymerase Rpb1 funnel domain / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / Pol I subunit A12, C-terminal zinc ribbon / : / RNA polymerase I, Rpa2 specific domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Enzyme I; Chain A, domain 2 / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Tetracycline Repressor; domain 2 / Helix Hairpins / Gyrase A; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / Homeodomain-like / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit
類似検索 - ドメイン・相同性
DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 ...DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA49
類似検索 - 構成要素
生物種SACCHAROMYCES CEREVISIAE (パン酵母)
手法X線回折 / シンクロトロン / 多波長異常分散 / 解像度: 2.8 Å
データ登録者Engel, C. / Sainsbury, S. / Cheung, A.C. / Kostrewa, D. / Cramer, P.
引用ジャーナル: Nature / 年: 2013
タイトル: RNA Polymerase I Structure and Transcription Regulation.
著者: Engel, C. / Sainsbury, S. / Cheung, A.C. / Kostrewa, D. / Cramer, P.
履歴
登録2013年8月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02013年10月23日Provider: repository / タイプ: Initial release
改定 1.12013年11月6日Group: Database references
改定 1.22015年8月19日Group: Derived calculations
改定 1.32024年10月23日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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 / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2B" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "PF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "PI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "VC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
1: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
2: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
3: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
4: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
A: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
B: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
O: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
P: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
Q: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
R: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
S: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
T: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
U: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
V: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
W: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
X: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
Y: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
Z: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,254,19546
ポリマ－1,253,08730
非ポリマー1,10816
水4,720262
1
A: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
B: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
O: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)627,09723
ポリマ－626,54315
非ポリマー5548
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area99110 Å2
ΔGint-545.1 kcal/mol
Surface area204050 Å2
手法PQS
2
1: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
2: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
3: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
4: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
P: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
Q: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
R: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
S: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
T: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
U: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
V: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
W: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
X: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
Y: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
Z: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)627,09723
ポリマ－626,54315
非ポリマー5548
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area98310 Å2
ΔGint-543.3 kcal/mol
Surface area203550 Å2
手法PQS
単位格子
Length a, b, c (Å)122.740, 139.020, 209.550
Angle α, β, γ (deg.)108.06, 95.40, 93.85
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214
115
215
116
216
117
217
118
218
119
219
120
220
121
221
122
222
123
223
124
224
125
225
126
226
127
227
128
228
129
229
130
230
131
231
132
232
133
233
134
234
135
235
136
236
137
237
138
238
139
239
140
240
141
241
142
242
143
243
144
244

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESSEQ 1:84
211CHAIN P AND RESSEQ 1:84
112CHAIN A AND RESSEQ 85:139
212CHAIN P AND RESSEQ 85:139
113CHAIN A AND RESSEQ 176:272
213CHAIN P AND RESSEQ 176:272
114CHAIN A AND RESSEQ 296:363
214CHAIN P AND RESSEQ 296:363
115CHAIN A AND RESSEQ 364:380
215CHAIN P AND RESSEQ 364:380
116CHAIN A AND RESSEQ 381:441
216CHAIN P AND RESSEQ 381:441
117CHAIN A AND RESSEQ 442:477
217CHAIN P AND RESSEQ 442:477
118CHAIN A AND RESSEQ 478:652
218CHAIN P AND RESSEQ 478:652
119CHAIN A AND RESSEQ 653:826
219CHAIN P AND RESSEQ 653:826
1110CHAIN A AND RESSEQ 827:989
2110CHAIN P AND RESSEQ 827:989
1111CHAIN A AND RESSEQ 990:1028
2111CHAIN P AND RESSEQ 990:1028
1112CHAIN A AND RESSEQ 1029:1152
2112CHAIN P AND RESSEQ 1029:1152
1113CHAIN A AND RESSEQ 1160:1204
2113CHAIN P AND RESSEQ 1160:1204
1114CHAIN A AND RESSEQ 1213:1337
2114CHAIN P AND RESSEQ 1213:1337
1115CHAIN A AND RESSEQ 1361:1395
2115CHAIN P AND RESSEQ 1361:1395
1116CHAIN A AND RESSEQ 1596:1664
2116CHAIN P AND RESSEQ 1596:1664
1117CHAIN B AND RESSEQ 8:79
2117CHAIN Q AND RESSEQ 8:79
1118CHAIN B AND RESSEQ 88:204
2118CHAIN Q AND RESSEQ 88:204
1119CHAIN B AND RESSEQ 205:404
2119CHAIN Q AND RESSEQ 205:404
1120CHAIN B AND RESSEQ 405:489
2120CHAIN Q AND RESSEQ 405:489
1121CHAIN B AND RESSEQ 490:697
2121CHAIN Q AND RESSEQ 490:697
1122CHAIN B AND RESSEQ 698:798
2122CHAIN Q AND RESSEQ 698:798
1123CHAIN B AND RESSEQ 799:910
2123CHAIN Q AND RESSEQ 799:910
1124CHAIN B AND RESSEQ 911:1038
2124CHAIN Q AND RESSEQ 911:1038
1125CHAIN B AND RESSEQ 1039:1203
2125CHAIN Q AND RESSEQ 1039:1203
1126CHAIN C AND RESSEQ 31:76
2126CHAIN R AND RESSEQ 31:76
1127CHAIN C AND RESSEQ 77:220
2127CHAIN R AND RESSEQ 77:220
1128CHAIN C AND RESSEQ 221:334
2128CHAIN R AND RESSEQ 221:334
1129CHAIN D
2129CHAIN S
1130CHAIN G AND RESSEQ 14:127
2130CHAIN V AND RESSEQ 14:127
1131CHAIN G AND RESSEQ 128:250
2131CHAIN V AND RESSEQ 128:250
1132CHAIN O AND RESSEQ 265:315
2132CHAIN 4 AND RESSEQ 265:315
1133CHAIN E AND RESSEQ 5:147
2133CHAIN T AND RESSEQ 5:147
1134CHAIN E AND RESSEQ 148:215
2134CHAIN T AND RESSEQ 148:215
1135CHAIN F
2135CHAIN U
1136CHAIN H
2136CHAIN W
1137CHAIN I AND RESSEQ 2:74
2137CHAIN X AND RESSEQ 2:74
1138CHAIN I AND RESSEQ 75:125
2138CHAIN X AND RESSEQ 75:125
1139CHAIN J
2139CHAIN Y
1140CHAIN K
2140CHAIN Z
1141CHAIN L
2141CHAIN 1
1142CHAIN M
2142CHAIN 2
1143CHAIN N AND RESSEQ 22:140
2143CHAIN 3 AND RESSEQ 22:140
1144CHAIN N AND RESSEQ 141:180
2144CHAIN 3 AND RESSEQ 141:180

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44

NCS oper: (Code: given
Matrix: (-0.9923, -0.1217, -0.02281), (-0.1221, 0.9923, 0.02118), (0.02006, 0.0238, -0.9995)
ベクター: 106.6, 7.927, 212.8)

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要素

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5種, 10分子 1LETFUHWJY

#1: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC4 / ABC10-ALPHA / RPB12


分子量: 7729.969 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P40422
#9: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 27 KDA POLYPEPTIDE / RPB5


分子量: 25117.094 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P20434
#10: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 23 KDA POLYPEPTIDE / RPB6


分子量: 17931.834 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P20435
#11: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 14.5 KDA POLYPEPTIDE / RPB8


分子量: 16525.363 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P20436
#13: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 8.3 KDA POLYPEPTIDE / RPB10


分子量: 8290.732 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P22139

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DNA-DIRECTED RNA POLYMERASE I SUBUNIT ... , 7種, 16分子 2M3N4GOVAPBQDSIX

#2: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 / A49 / DNA-DIRECTED RNA POLYMERASE I 49 KDA POLYPEPTIDE


分子量: 46721.707 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: Q01080
#3: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 / A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POLYPEPTIDE / A34.5 / A34.5


分子量: 26933.518 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P47006
#4: タンパク質
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 / A43 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 36 KDA POLYPEPTIDE / A43


分子量: 36264.852 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P46669
#5: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190 / A190 / DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT


分子量: 186676.969 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P10964, DNA-directed RNA polymerase
#6: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 / DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DNA-DIRECTED RNA POLYMERASE I ...DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DNA-DIRECTED RNA POLYMERASE I POLYPEPTIDE 2 / RNA POLYMERASE I SUBUNIT 2 / A135


分子量: 135910.328 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P22138, DNA-directed RNA polymerase
#8: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14 / A14 / DNA-DIRECTED RNA POLYMERASE I 14 KDA POLYPEPTIDE / A14


分子量: 14599.128 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P50106
#12: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 / A12 / A12.2 / DNA-DIRECTED RNA POLYMERASE I 13.7 KDA POLYPEPTIDE / A12.2


分子量: 13676.566 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P32529

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DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ... , 2種, 4分子 CRKZ

#7: タンパク質 DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 / RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RN A POLYMERASES I AND III 40 KDA ...RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RN A POLYMERASES I AND III 40 KDA POLYPEPTIDE / AC40 / C40 / AC40


分子量: 37732.613 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P07703
#14: タンパク質 DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2 / RNA POLYMERASES I AND III SUBUNIT AC2 / DNA-DIRECTED R NA POLYMERASES I AND III 16 KDA POLYPEPTIDE ...RNA POLYMERASES I AND III SUBUNIT AC2 / DNA-DIRECTED R NA POLYMERASES I AND III 16 KDA POLYPEPTIDE / RPA19 / AC19


分子量: 16167.860 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: CB010 / 参照: UniProt: P28000

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非ポリマー , 3種, 278分子

#15: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Zn
#16: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
#17: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 262 / 由来タイプ: 天然 / 式: H2O

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 4

-
試料調製

結晶マシュー密度: 2.85 Å3/Da / 溶媒含有率: 56.9 % / 解説: NONE
結晶化pH: 7
詳細: 10% PEG4000, 300MM AMMONIUM ACETATE, 50MM HEPES PH 7.5, 5MM TCEP

-
データ収集

回折
ID平均測定温度 (K)Crystal-ID
11001
21001
放射光源
由来サイトビームラインID波長
シンクロトロンSLS X10SA11
シンクロトロンSLS X06SA21.28288
検出器
タイプID検出器
DECTRIS PILATUS 6M1PIXEL
DECTRIS PILATUS 6M2PIXEL
放射
IDプロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
放射波長
ID波長 (Å)相対比
111
21.282881
反射解像度: 2.8→40 Å / Num. obs: 320814 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / 冗長度: 13.1 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 9.61
反射 シェル解像度: 2.8→2.87 Å / 冗長度: 11.5 % / Mean I/σ(I) obs: 1.52 / % possible all: 99.8

-
解析

ソフトウェア
名称分類
XDSデータ削減
XDSデータスケーリング
autoSHARP位相決定
PARROT位相決定
PHENIX精密化
精密化構造決定の手法: 多波長異常分散
開始モデル: NONE

解像度: 2.8→39.292 Å / SU ML: 0.39 / σ(F): 1.99 / 位相誤差: 23.43 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2099 6493 2 %
Rwork0.1689 --
obs0.1697 320815 99.91 %
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
精密化ステップサイクル: LAST / 解像度: 2.8→39.292 Å
タンパク質核酸リガンド溶媒全体
原子数68821 0 24 262 69107
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0170209
X-RAY DIFFRACTIONf_angle_d1.24194762
X-RAY DIFFRACTIONf_dihedral_angle_d16.31826576
X-RAY DIFFRACTIONf_chiral_restr0.08410577
X-RAY DIFFRACTIONf_plane_restr0.00512274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A625X-RAY DIFFRACTIONPOSITIONAL
12P625X-RAY DIFFRACTIONPOSITIONAL0.075
21A475X-RAY DIFFRACTIONPOSITIONAL
22P475X-RAY DIFFRACTIONPOSITIONAL0.037
31A783X-RAY DIFFRACTIONPOSITIONAL
32P783X-RAY DIFFRACTIONPOSITIONAL0.055
41A427X-RAY DIFFRACTIONPOSITIONAL
42P427X-RAY DIFFRACTIONPOSITIONAL0.092
51A141X-RAY DIFFRACTIONPOSITIONAL
52P141X-RAY DIFFRACTIONPOSITIONAL0.035
61A489X-RAY DIFFRACTIONPOSITIONAL
62P489X-RAY DIFFRACTIONPOSITIONAL0.101
71A279X-RAY DIFFRACTIONPOSITIONAL
72P279X-RAY DIFFRACTIONPOSITIONAL0.042
81A1367X-RAY DIFFRACTIONPOSITIONAL
82P1367X-RAY DIFFRACTIONPOSITIONAL0.041
91A1368X-RAY DIFFRACTIONPOSITIONAL
92P1368X-RAY DIFFRACTIONPOSITIONAL0.042
101A1220X-RAY DIFFRACTIONPOSITIONAL
102P1220X-RAY DIFFRACTIONPOSITIONAL0.042
111A316X-RAY DIFFRACTIONPOSITIONAL
112P316X-RAY DIFFRACTIONPOSITIONAL0.054
121A1012X-RAY DIFFRACTIONPOSITIONAL
122P1012X-RAY DIFFRACTIONPOSITIONAL0.041
131A341X-RAY DIFFRACTIONPOSITIONAL
132P341X-RAY DIFFRACTIONPOSITIONAL0.041
141A921X-RAY DIFFRACTIONPOSITIONAL
142P921X-RAY DIFFRACTIONPOSITIONAL0.043
151A290X-RAY DIFFRACTIONPOSITIONAL
152P290X-RAY DIFFRACTIONPOSITIONAL0.083
161A524X-RAY DIFFRACTIONPOSITIONAL
162P524X-RAY DIFFRACTIONPOSITIONAL0.048
171B544X-RAY DIFFRACTIONPOSITIONAL
172Q544X-RAY DIFFRACTIONPOSITIONAL0.038
181B885X-RAY DIFFRACTIONPOSITIONAL
182Q885X-RAY DIFFRACTIONPOSITIONAL0.039
191B1632X-RAY DIFFRACTIONPOSITIONAL
192Q1632X-RAY DIFFRACTIONPOSITIONAL0.05
201B677X-RAY DIFFRACTIONPOSITIONAL
202Q677X-RAY DIFFRACTIONPOSITIONAL0.092
211B1651X-RAY DIFFRACTIONPOSITIONAL
212Q1651X-RAY DIFFRACTIONPOSITIONAL0.068
221B787X-RAY DIFFRACTIONPOSITIONAL
222Q787X-RAY DIFFRACTIONPOSITIONAL0.045
231B865X-RAY DIFFRACTIONPOSITIONAL
232Q865X-RAY DIFFRACTIONPOSITIONAL0.03
241B1004X-RAY DIFFRACTIONPOSITIONAL
242Q1004X-RAY DIFFRACTIONPOSITIONAL0.055
251B1216X-RAY DIFFRACTIONPOSITIONAL
252Q1216X-RAY DIFFRACTIONPOSITIONAL0.047
261C377X-RAY DIFFRACTIONPOSITIONAL
262R377X-RAY DIFFRACTIONPOSITIONAL0.145
271C1121X-RAY DIFFRACTIONPOSITIONAL
272R1121X-RAY DIFFRACTIONPOSITIONAL0.048
281C915X-RAY DIFFRACTIONPOSITIONAL
282R915X-RAY DIFFRACTIONPOSITIONAL0.032
291D459X-RAY DIFFRACTIONPOSITIONAL
292S459X-RAY DIFFRACTIONPOSITIONAL0.029
301G890X-RAY DIFFRACTIONPOSITIONAL
302V890X-RAY DIFFRACTIONPOSITIONAL0.036
311G618X-RAY DIFFRACTIONPOSITIONAL
312V618X-RAY DIFFRACTIONPOSITIONAL0.058
321O404X-RAY DIFFRACTIONPOSITIONAL
3224404X-RAY DIFFRACTIONPOSITIONAL0.033
331E1161X-RAY DIFFRACTIONPOSITIONAL
332T1161X-RAY DIFFRACTIONPOSITIONAL0.027
341E565X-RAY DIFFRACTIONPOSITIONAL
342T565X-RAY DIFFRACTIONPOSITIONAL0.065
351F823X-RAY DIFFRACTIONPOSITIONAL
352U823X-RAY DIFFRACTIONPOSITIONAL0.037
361H1052X-RAY DIFFRACTIONPOSITIONAL
362W1052X-RAY DIFFRACTIONPOSITIONAL0.032
371I516X-RAY DIFFRACTIONPOSITIONAL
372X516X-RAY DIFFRACTIONPOSITIONAL0.043
381I384X-RAY DIFFRACTIONPOSITIONAL
382X384X-RAY DIFFRACTIONPOSITIONAL0.032
391J570X-RAY DIFFRACTIONPOSITIONAL
392Y570X-RAY DIFFRACTIONPOSITIONAL0.036
401K786X-RAY DIFFRACTIONPOSITIONAL
402Z786X-RAY DIFFRACTIONPOSITIONAL0.055
411L353X-RAY DIFFRACTIONPOSITIONAL
4121353X-RAY DIFFRACTIONPOSITIONAL0.029
421M814X-RAY DIFFRACTIONPOSITIONAL
4222814X-RAY DIFFRACTIONPOSITIONAL0.031
431N816X-RAY DIFFRACTIONPOSITIONAL
4323816X-RAY DIFFRACTIONPOSITIONAL0.031
441N320X-RAY DIFFRACTIONPOSITIONAL
4423320X-RAY DIFFRACTIONPOSITIONAL0.032
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.34852120.31810451X-RAY DIFFRACTION100
2.8318-2.86510.33972180.310460X-RAY DIFFRACTION100
2.8651-2.90.32252360.285810483X-RAY DIFFRACTION100
2.9-2.93670.30652360.265410465X-RAY DIFFRACTION100
2.9367-2.97540.30112110.253910453X-RAY DIFFRACTION100
2.9754-3.01610.31462230.254910481X-RAY DIFFRACTION100
3.0161-3.05920.27032300.247610455X-RAY DIFFRACTION100
3.0592-3.10480.31742360.246910423X-RAY DIFFRACTION100
3.1048-3.15330.33042080.245910561X-RAY DIFFRACTION100
3.1533-3.2050.28172100.243110452X-RAY DIFFRACTION100
3.205-3.26020.27062480.225510466X-RAY DIFFRACTION100
3.2602-3.31950.29451980.220410572X-RAY DIFFRACTION100
3.3195-3.38330.25872010.210910465X-RAY DIFFRACTION100
3.3833-3.45230.24782170.199410411X-RAY DIFFRACTION100
3.4523-3.52740.2262270.189310479X-RAY DIFFRACTION100
3.5274-3.60940.23812060.185810565X-RAY DIFFRACTION100
3.6094-3.69950.2191970.169310428X-RAY DIFFRACTION100
3.6995-3.79950.21672150.162710469X-RAY DIFFRACTION100
3.7995-3.91120.20622090.159210507X-RAY DIFFRACTION100
3.9112-4.03730.21662170.152610449X-RAY DIFFRACTION100
4.0373-4.18150.20152100.147810538X-RAY DIFFRACTION100
4.1815-4.34870.17352150.133610527X-RAY DIFFRACTION100
4.3487-4.54630.15912060.129810456X-RAY DIFFRACTION100
4.5463-4.78560.16652200.125510513X-RAY DIFFRACTION100
4.7856-5.08490.16882270.126910452X-RAY DIFFRACTION100
5.0849-5.47650.15552230.133810483X-RAY DIFFRACTION100
5.4765-6.02590.1852000.143710500X-RAY DIFFRACTION100
6.0259-6.89380.1962040.149110504X-RAY DIFFRACTION100
6.8938-8.670.17112220.138210477X-RAY DIFFRACTION100
8.67-39.29630.15542110.146410377X-RAY DIFFRACTION99
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)
10.8457-0.28590.10470.51880.02050.32640.01240.13860.3649-0.0644-0.0437-0.1187-0.14510.0404-00.5303-0.0410.00240.48750.09650.630449.5617129.4574160.767
20.7875-0.0413-0.05850.9547-0.28090.99060.0092-0.0915-0.12670.1126-0.03810.10660.13-0.0708-0.00010.4925-0.03030.00120.53230.04950.486615.469989.3582163.8487
31.3251-0.0103-0.38741.22510.08521.1674-0.01620.0912-0.4279-0.0799-0.077-0.23590.16470.1425-0.00020.52770.029-0.01110.58720.03230.633640.157869.4737136.6994
41.1614-0.0249-0.00471.00420.40491.20390.0580.8883-0.3307-0.5104-0.22570.19510.2821-0.3358-0.01090.88910.0662-0.20871.3082-0.1350.685.380681.6845107.1565
51.0481-0.2490.31121.06610.03450.7146-0.0843-0.5060.12750.56020.2702-0.6160.14310.31170.00020.89330.1725-0.30011.0172-0.14730.9531100.735994.2562206.2561
60.12550.02940.00450.08070.04470.0294-0.3526-0.5349-1.12980.25960.28520.31211.05090.1412-0.00171.08190.1868-0.07610.91050.19610.8685.549968.8476202.3236
70.06360.08330.04330.12520.10130.14870.0940.19020.393-0.1858-0.00790.3877-0.3311-0.55210.00010.97290.08490.02430.84460.17910.746145.293293.4795201.7095
80.08120.11110.09190.18970.17420.1661-0.15260.1593-0.0210.1446-0.36820.48750.3899-0.79020.00060.8157-0.10070.05290.8673-0.08130.757930.7226111.5067182.3912
90.52110.47420.3050.76170.21010.619-0.0249-0.0379-0.5020.00840.0499-0.19440.403-0.15360.00010.88540.0083-0.05510.79630.17720.684455.734667.7819203.1779
100.8446-0.4506-0.20610.81370.18870.9853-0.1423-0.0734-0.09460.16020.0743-0.11460.20810.12790.00010.59220.0288-0.06650.57870.04040.557279.910385.4226183.0671
110.4143-0.05940.24160.46460.19610.2566-0.1556-0.11760.19120.20330.2497-0.26270.11280.18470.00010.52680.0372-0.15030.6563-0.04540.632182.6974106.7574193.855
120.6955-0.1427-0.00110.76690.27390.68740.0244-0.31640.34120.1424-0.09640.379-0.305-0.3942-0.00020.74130.17140.08330.7904-0.15611.0088-3.01140.1705183.9891
130.79550.05630.11030.72330.23390.6128-0.049-0.11720.2240.0755-0.18510.4095-0.2239-0.1741-0.01140.75180.04590.03310.595-0.12290.788440.5961125.924754.8951
140.783-0.04730.00661.11740.59021.44260.00140.1705-0.12020.0727-0.0093-0.07130.15210.23840.00030.63660.00710.04330.63580.02510.472579.869390.325653.1921
151.3649-0.0962-0.30611.4060.08481.27280.0506-0.0261-0.4180.1393-0.13420.28910.2733-0.142-0.00030.8831-0.0720.02740.5854-0.00290.635557.100167.258179.3932
160.7712-0.00770.23570.294-0.70511.54060.088-0.3952-0.18250.0414-0.107-0.02070.30590.36310.00011.0382-0.0027-0.08780.97250.040.57288.569385.1618111.0841
170.86790.37480.22711.03440.26150.61-0.11130.3664-0.0835-0.4326-0.36120.9151-0.1769-0.5728-0.02620.83750.1021-0.23461.4629-0.65121.7693-4.163883.51528.1337
180.1241-0.11460.17010.1447-0.22260.34420.1456-0.174-0.82690.0087-0.29110.58690.6624-0.05110.02220.8221-0.09760.05921.2175-0.68471.731713.652460.301813.3168
190.0667-0.0593-0.00070.1026-0.07110.10040.05780.03280.17410.2879-0.25020.1639-0.210.12430.00110.7564-0.047-0.09080.8881-0.32070.917948.112487.195414.4203
200.0859-0.0350.08720.1205-0.09280.1181-0.1485-0.1992-0.24310.0328-0.3464-0.29520.18710.69430.0011.09810.07110.03441.00960.04980.93262.0321109.828134.3912
210.6127-0.52380.39190.5793-0.28780.6648-0.0592-0.1298-0.60070.007-0.11360.57620.38850.19470.00030.72-0.00130.0620.9038-0.31231.087543.413362.787213.4834
220.4579-0.01040.05980.64830.03770.6098-0.0896-0.0377-0.33570.1852-0.25490.51630.2106-0.30540.00030.6041-0.09760.16270.8681-0.38611.296916.255577.795732.5526
230.1873-0.1143-0.06640.2175-0.15660.2894-0.22010.1501-0.0121-0.1077-0.12490.602-0.0463-0.5024-0.02140.54310.1145-0.19790.9463-0.44441.302411.422698.388121.3402
240.67020.15410.12660.597-0.25980.6047-0.03220.50910.5471-0.2255-0.0115-0.1849-0.5540.4894-0.00021.1027-0.30280.04030.9030.20320.783691.5535142.785232.9817
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 654:1013 OR RESID 1361:1367) OR CHAIN B AND (RESID 8:209 OR RESID 400:553 OR RESID 647:1068) OR CHAIN C OR CHAIN J OR CHAIN K OR CHAIN L OR CHAIN N AND RESID 147:180
2X-RAY DIFFRACTION2CHAIN A AND (RESID 477:653 OR RESID 1014:1261 OR RESID 1368:1395 OR RESID 1500:1608) OR CHAIN B AND RESID 1069:1092 OR CHAIN E OR CHAIN F AND RESID 73:154
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1:476 OR RESID 1609:1649 OR RESID 3001:3002) OR CHAIN B AND (RESID 1093-1203 OR RESID 3001) OR CHAIN O
4X-RAY DIFFRACTION4CHAIN A AND RESID 1650:1664 OR CHAIN D OR CHAIN F AND RESID 55:72 OR CHAIN G
5X-RAY DIFFRACTION5CHAIN M OR CHAIN N AND RESID 25:146
6X-RAY DIFFRACTION6CHAIN I AND (RESID 2:52 OR RESID 3001)
7X-RAY DIFFRACTION7CHAIN I AND RESID 53:78
8X-RAY DIFFRACTION8CHAIN I AND (RESID 79:125 OR RESID 3002)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 1262:1337 OR RESID 1440:1499)
10X-RAY DIFFRACTION10CHAIN B AND RESID 210:399
11X-RAY DIFFRACTION11CHAIN B AND RESID 554:646
12X-RAY DIFFRACTION12CHAIN H
13X-RAY DIFFRACTION13CHAIN P AND (RESID 654:1013 OR RESID 1361:1367) OR CHAIN Q AND (RESID 8:209 OR RESID 400:553 OR RESID 647:1068) OR CHAIN R OR CHAIN Y OR CHAIN Z OR CHAIN 1 OR CHAIN 3 AND RESID 147:181
14X-RAY DIFFRACTION14CHAIN P AND (RESID 477:653 OR RESID 1014:1261 OR RESID 1368:1395 OR RESID 1500:1608) OR CHAIN Q AND RESID 1069:1092 OR CHAIN T OR CHAIN U AND RESID 73:154
15X-RAY DIFFRACTION15CHAIN P AND (RESID 1:476 OR RESID 1609:1649 OR RESID 3001:3002) OR CHAIN Q AND (RESID 1093-1203 OR RESID 3001) OR CHAIN 4
16X-RAY DIFFRACTION16CHAIN P AND RESID 1650:1664 OR CHAIN S OR CHAIN U AND RESID 55:72 OR CHAIN V
17X-RAY DIFFRACTION17CHAIN 2 OR CHAIN 3 AND RESID 25:146
18X-RAY DIFFRACTION18CHAIN X AND (RESID 2:52 OR RESID 3001)
19X-RAY DIFFRACTION19CHAIN X AND RESID 53:78
20X-RAY DIFFRACTION20CHAIN X AND (RESID 79:125 OR RESID 3002)
21X-RAY DIFFRACTION21CHAIN P AND (RESID 1262:1337 OR RESID 1440:1499)
22X-RAY DIFFRACTION22CHAIN Q AND RESID 210:399
23X-RAY DIFFRACTION23CHAIN Q AND RESID 554:646
24X-RAY DIFFRACTION24CHAIN W

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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