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- PDB-4v8s: Archaeal RNAP-DNA binary complex at 4.32Ang -

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基本情報

登録情報
データベース: PDB / ID: 4v8s
タイトルArchaeal RNAP-DNA binary complex at 4.32Ang
要素
  • (DNA-DIRECTED RNA ...) x 9
  • (RNA POLYMERASE SUBUNIT ...) x 4
  • 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
  • 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
キーワードTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSCRIPTION
機能・相同性
機能・相同性情報


RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / nucleotidyltransferase activity / DNA-templated transcription initiation ...RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / nucleotidyltransferase activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
類似検索 - 分子機能
RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 ...RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / 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. / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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, 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 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Nucleic acid-binding, OB-fold
類似検索 - ドメイン・相同性
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13
類似検索 - 構成要素
生物種SULFOLOBUS SHIBATAE B12 (古細菌)
SYNTHETIC CONSTRUCT (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.323 Å
データ登録者Wojtas, M.N. / Mogni, M. / Millet, O. / Bell, S.D. / Abrescia, N.G.A.
引用
ジャーナル: Nucleic Acids Res. / 年: 2012
タイトル: Structural and Functional Analyses of the Interaction of Archaeal RNA Polymerase with DNA.
著者: Wojtas, M.N. / Mogni, M. / Millet, O. / Bell, S.D. / Abrescia, N.G.A.
#1: ジャーナル: Biochem.Soc.Trans. / 年: 2011
タイトル: Archaeal RNA Polymerase: The Influence of the Protruding Stalk in Crystal Packing and Preliminary Biophysical Analysis of the Rpo13 Subunit.
著者: Wojtas, M. / Peralta, B. / Ondiviela, M. / Mogni, M. / Bell, S.D. / Abrescia, N.G.A.
#2: ジャーナル: Plos Biol. / 年: 2009
タイトル: Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
著者: Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.A.
履歴
登録2012年7月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02014年7月9日Provider: repository / タイプ: Initial release
置き換え2014年12月10日ID: 4B1O, 4B1P
改定 1.12014年12月10日Group: Other
改定 1.22019年11月20日Group: Advisory / Derived calculations
カテゴリ: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
改定 1.32024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "RQ" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "RQ" 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 "TB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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

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集合体

登録構造単位
AC: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
AD: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
AI: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
AJ: RNA POLYMERASE SUBUNIT 13
AM: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
AO: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
AR: DNA-DIRECTED RNA POLYMERASE
AS: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
AT: RNA POLYMERASE SUBUNIT 7
AU: RNA POLYMERASE SUBUNIT 4
AV: RNA POLYMERASE SUBUNIT 8
AW: DNA-DIRECTED RNA POLYMERASE
AX: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
AY: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
AZ: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
BA: DNA-DIRECTED RNA POLYMERASE
BB: DNA-DIRECTED RNA POLYMERASE
BC: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
BD: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
BE: RNA POLYMERASE SUBUNIT 7
BF: RNA POLYMERASE SUBUNIT 4
BG: RNA POLYMERASE SUBUNIT 8
BH: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
BK: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
BL: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
BN: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
BP: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
BQ: RNA POLYMERASE SUBUNIT 13
BR: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
BS: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)831,15846
ポリマ－829,62130
非ポリマー1,53716
水00
1
AC: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
AD: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
AI: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
AJ: RNA POLYMERASE SUBUNIT 13
AM: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
AO: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
AR: DNA-DIRECTED RNA POLYMERASE
AS: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
AT: RNA POLYMERASE SUBUNIT 7
AU: RNA POLYMERASE SUBUNIT 4
AV: RNA POLYMERASE SUBUNIT 8
AW: DNA-DIRECTED RNA POLYMERASE
AX: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
AY: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
AZ: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)415,57923
ポリマ－414,81115
非ポリマー7688
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
BA: DNA-DIRECTED RNA POLYMERASE
BB: DNA-DIRECTED RNA POLYMERASE
BC: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
BD: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
BE: RNA POLYMERASE SUBUNIT 7
BF: RNA POLYMERASE SUBUNIT 4
BG: RNA POLYMERASE SUBUNIT 8
BH: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
BK: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
BL: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
BN: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
BP: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
BQ: RNA POLYMERASE SUBUNIT 13
BR: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
BS: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)415,57923
ポリマ－414,81115
非ポリマー7688
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)134.134, 199.416, 214.246
Angle α, β, γ (deg.)90.00, 103.54, 90.00
Int Tables number4
Space group name H-MP1211
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

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN BB AND (RESSEQ 7:510 OR RESSEQ 516:821 OR RESSEQ...
211CHAIN AR AND (RESSEQ 7:510 OR RESSEQ 516:821 OR RESSEQ...
112CHAIN AA AND (RESSEQ 3:222 OR RESSEQ 228:879 OR RESSEQ...
212CHAIN BW AND (RESSEQ 3:222 OR RESSEQ 228:879 OR RESSEQ...
113CHAIN BC AND (RESSEQ 6:86 OR RESSEQ 100:394 ) AND (NOT ELEMENT H)
213CHAIN AY AND (RESSEQ 6:86 OR RESSEQ 100:394 ) AND (NOT ELEMENT H)
114CHAIN BD AND (RESSEQ 2:263 OR RESSEQ 1001:1001 ) AND (NOT ELEMENT H)
214CHAIN AS AND (RESSEQ 2:263 OR RESSEQ 1001:1001 ) AND (NOT ELEMENT H)
115CHAIN BE AND (RESSEQ 1:151 OR RESSEQ 159:178 ) AND (NOT ELEMENT H)
215CHAIN AT AND (RESSEQ 1:151 OR RESSEQ 159:178 ) AND (NOT ELEMENT H)
116CHAIN BG AND (RESSEQ 5:117 ) AND (NOT ELEMENT H)
216CHAIN AV AND (RESSEQ 5:117 ) AND (NOT ELEMENT H)
117CHAIN BL AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
217CHAIN AM AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
118CHAIN BF AND (RESSEQ 3:107 ) AND (NOT ELEMENT H)
218CHAIN AU AND (RESSEQ 3:107 ) AND (NOT ELEMENT H)
119CHAIN BK AND (RESSEQ 11:94 ) AND (NOT ELEMENT H)
219CHAIN AI AND (RESSEQ 11:94 ) AND (NOT ELEMENT H)
1110CHAIN BH AND (RESSEQ 8:83 ) AND (NOT ELEMENT H)
2110CHAIN AZ AND (RESSEQ 8:83 ) AND (NOT ELEMENT H)
1111CHAIN BN AND (RESSEQ 1:65 OR RESSEQ 100:100 ) AND (NOT ELEMENT H)
2111CHAIN AO AND (RESSEQ 1:65 OR RESSEQ 100:100 ) AND (NOT ELEMENT H)
1112CHAIN BQ AND (RESSEQ 32:81 ) AND (NOT ELEMENT H)
2112CHAIN AJ AND (RESSEQ 33:81 ) AND (NOT ELEMENT H)
1113CHAIN BP AND (RESSEQ 5:48 OR RESSEQ 50:50 ) AND (NOT ELEMENT H)
2113CHAIN AX AND (RESSEQ 5:48 OR RESSEQ 50:50 ) AND (NOT ELEMENT H)
1114CHAIN BR AND (RESSEQ 1:14 ) AND (NOT ELEMENT H)
2114CHAIN AC AND (RESSEQ 1:13 ) AND (NOT ELEMENT H)
1115CHAIN BS AND (RESSEQ 2:17 ) AND (NOT ELEMENT H)
2115CHAIN AD AND (RESSEQ 3:17 ) AND (NOT ELEMENT H)

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixベクター
1given(0.885368, -0.000197, 0.46489), (-0.000404, -1, 0.000346), (0.46489, -0.000495, -0.885368)-17.5242, 0.97464, 73.0054
2given(0.884904, 0.000322, 0.465773), (-0.000458, -0.999999, 0.001562), (0.465773, -0.001595, -0.884903)-17.8278, 0.92819, 72.877
3given(0.888171, -0.000465, 0.459512), (8.0E-5, -0.999999, -0.001167), (0.459513, 0.001074, -0.888171)-17.7753, 0.87557, 72.9867
4given(0.885738, 0.008986, 0.464099), (0.007421, -0.999959, 0.005199), (0.464126, -0.001161, -0.885768)-18.4488, 0.15513, 73.5251
5given(0.886208, 0.007163, 0.463232), (9.6E-5, -0.999883, 0.015278), (0.463288, -0.013495, -0.886105)-18.6175, 0.0334, 73.7934
6given(0.890748, -0.011391, 0.454355), (-0.011904, -0.999928, -0.001733), (0.454342, -0.003865, -0.890819)-17.8369, 2.09797, 74.3844
7given(0.886512, -0.00033, 0.462705), (-0.001808, -0.999995, 0.002751), (0.462701, -0.003275, -0.886508)-18.1802, 0.99672, 73.6236
8given(0.874996, -0.002785, 0.484122), (0.018672, -0.999045, -0.039497), (0.48377, 0.043599, -0.874109)-18.6897, 3.15934, 67.7999
9given(0.884357, -0.001604, 0.466809), (-0.000526, -0.999997, -0.002439), (0.466811, 0.001912, -0.884355)-18.1468, 1.06673, 72.4899
10given(0.886773, 0.010436, 0.462087), (0.010984, -0.999939, 0.001504), (0.462074, 0.003742, -0.886834)-18.163, 0.47149, 72.6002
11given(0.885157, 0.005504, 0.46526), (-0.001872, -0.99988, 0.015391), (0.465288, -0.014494, -0.88504)-18.0104, 0.86423, 74.1794
12given(0.890021, -0.016838, 0.455609), (-0.031801, -0.999177, 0.025196), (0.454809, -0.036914, -0.889823)-17.372, 0.091, 74.3282
13given(0.88678, -0.001316, 0.462189), (-0.005319, -0.999959, 0.007359), (0.46216, -0.008984, -0.886751)-17.4611, 1.28646, 74.0631
14given(0.924118, -0.062296, 0.376995), (0.021083, -0.976805, -0.21309), (0.381525, 0.204869, -0.90137)-17.0414, 2.59576, 69.2878
15given(0.924327, -0.059168, 0.376987), (0.02366, -0.97712, -0.21137), (0.380867, 0.204295, -0.901778)-17.1388, 2.51038, 69.2964

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要素

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DNA鎖 , 2種, 4分子 ACBRADBS

#1: DNA鎖 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'


分子量: 4180.739 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物)
#2: DNA鎖 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'


分子量: 4994.292 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物)

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DNA-DIRECTED RNA ... , 9種, 18分子 AIBKAMBLAOBNARBBASBDAWBAAXBPAYBCAZBH

#3: タンパク質 DNA-DIRECTED RNA POLYMERASE SUBUNIT K


分子量: 10729.534 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO6 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB61, DNA-directed RNA polymerase
#5: タンパク質 DNA-DIRECTED RNA POLYMERASE SUBUNIT L


分子量: 10211.846 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO11 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB62, DNA-directed RNA polymerase
#6: タンパク質 DNA-DIRECTED RNA POLYMERASE SUBUNIT N


分子量: 7617.085 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO10 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB63, DNA-directed RNA polymerase
#7: タンパク質 DNA-DIRECTED RNA POLYMERASE


分子量: 127582.016 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO2 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB55, DNA-directed RNA polymerase
#8: タンパク質 DNA-DIRECTED RNA POLYMERASE SUBUNIT D


分子量: 30179.119 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO3 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB56, DNA-directed RNA polymerase
#12: タンパク質 DNA-DIRECTED RNA POLYMERASE


分子量: 99766.523 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO1N SUBUNIT / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB53, DNA-directed RNA polymerase
#13: タンパク質・ペプチド DNA-DIRECTED RNA POLYMERASE SUBUNIT P


分子量: 5606.951 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO12 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB64, DNA-directed RNA polymerase
#14: タンパク質 DNA-DIRECTED RNA POLYMERASE SUBUNIT A''


分子量: 43792.785 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO1C / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB54, DNA-directed RNA polymerase
#15: タンパク質 DNA-DIRECTED RNA POLYMERASE SUBUNIT H


分子量: 9688.296 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO5 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB60, DNA-directed RNA polymerase

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RNA POLYMERASE SUBUNIT ... , 4種, 8分子 AJBQATBEAUBFAVBG

#4: タンパク質 RNA POLYMERASE SUBUNIT 13


分子量: 12170.576 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB65
#9: タンパク質 RNA POLYMERASE SUBUNIT 7


分子量: 20328.703 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO7 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB57
#10: タンパク質 RNA POLYMERASE SUBUNIT 4


分子量: 12822.612 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPOF / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB58
#11: タンパク質 RNA POLYMERASE SUBUNIT 8


分子量: 15139.458 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO8 / 由来: (天然) SULFOLOBUS SHIBATAE B12 (古細菌) / 参照: UniProt: B8YB59

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非ポリマー , 3種, 16分子

#16: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Zn
#17: 化合物 ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe4S4
#18: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg

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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: 3.76 Å3/Da / 溶媒含有率: 67.27 % / 解説: NONE
結晶化pH: 6.5
詳細: PLEASE SEE PRIMARY REFERENCE AND WOJTAS MN & ABRESCIA NGA, SUBMITTED, pH 6.5

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データ収集

回折平均測定温度: 110 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: BM14 / 波長: 1.033
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 詳細: BENT COLLIMATING MIRROR AND TOROID
放射モノクロメーター: SI(111) / 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: 1.033 Å / 相対比: 1
反射解像度: 4.3→60 Å / Num. obs: 65048 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / 冗長度: 4.1 % / Biso Wilson estimate: 105.24 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 6
反射 シェル解像度: 4.3→4.45 Å / 冗長度: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 77.8

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解析

ソフトウェア
名称バージョン分類
PHASERモデル構築
PHENIX(PHENIX.REFINE)精密化
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 4AYB

4ayb


解像度: 4.323→50.424 Å / SU ML: 0.58 / σ(F): 1.34 / 位相誤差: 33.37 / 立体化学のターゲット値: ML
詳細: AS IN THE APO-RNAP STRUCTURE PDB 4AYB WE CAN SEE ADDITIONAL DENSITY BETWEEN ASP 178 AND GLU 444 IN CHAIN B -AND R- POSSIBLY ATTRIBUTABLE TO A DIVALENT ION
Rfactor反射数%反射
Rfree0.3105 3301 5.1 %
Rwork0.2917 --
obs0.2926 64957 88.56 %
溶媒の処理減衰半径: 0.89 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 114.371 Å2 / ksol: 0.358 e/Å3
原子変位パラメータBiso mean: 173.91 Å2
Baniso -1Baniso -2Baniso -3
1-62.6028 Å20 Å254.0591 Å2
2---26.0386 Å20 Å2
3----36.5642 Å2
精密化ステップサイクル: LAST / 解像度: 4.323→50.424 Å
タンパク質核酸リガンド溶媒全体
原子数27092 575 14 0 27681
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00556636
X-RAY DIFFRACTIONf_angle_d0.66776685
X-RAY DIFFRACTIONf_dihedral_angle_d12.91321764
X-RAY DIFFRACTIONf_chiral_restr0.048717
X-RAY DIFFRACTIONf_plane_restr0.0039618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11BB8757X-RAY DIFFRACTIONPOSITIONAL
12AR8757X-RAY DIFFRACTIONPOSITIONAL0.007
21BA6961X-RAY DIFFRACTIONPOSITIONAL
22AW6961X-RAY DIFFRACTIONPOSITIONAL0.011
31BC2906X-RAY DIFFRACTIONPOSITIONAL
32AY2906X-RAY DIFFRACTIONPOSITIONAL0.006
41BD2094X-RAY DIFFRACTIONPOSITIONAL
42AS2094X-RAY DIFFRACTIONPOSITIONAL0.01
51BE1359X-RAY DIFFRACTIONPOSITIONAL
52AT1359X-RAY DIFFRACTIONPOSITIONAL0.005
61BG901X-RAY DIFFRACTIONPOSITIONAL
62AV901X-RAY DIFFRACTIONPOSITIONAL0.008
71BL707X-RAY DIFFRACTIONPOSITIONAL
72AM707X-RAY DIFFRACTIONPOSITIONAL0.01
81BF827X-RAY DIFFRACTIONPOSITIONAL
82AU827X-RAY DIFFRACTIONPOSITIONAL0.007
91BK673X-RAY DIFFRACTIONPOSITIONAL
92AI673X-RAY DIFFRACTIONPOSITIONAL0.01
101BH624X-RAY DIFFRACTIONPOSITIONAL
102AZ624X-RAY DIFFRACTIONPOSITIONAL0.009
111BN522X-RAY DIFFRACTIONPOSITIONAL
112AO522X-RAY DIFFRACTIONPOSITIONAL0.008
121BQ417X-RAY DIFFRACTIONPOSITIONAL
122AJ417X-RAY DIFFRACTIONPOSITIONAL0.047
131BP358X-RAY DIFFRACTIONPOSITIONAL
132AX358X-RAY DIFFRACTIONPOSITIONAL0.003
141BR260X-RAY DIFFRACTIONPOSITIONAL
142AC260X-RAY DIFFRACTIONPOSITIONAL0.002
151BS315X-RAY DIFFRACTIONPOSITIONAL
152AD315X-RAY DIFFRACTIONPOSITIONAL0.009
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3226-4.4770.35142120.32113504X-RAY DIFFRACTION51
4.477-4.65610.3542840.31265445X-RAY DIFFRACTION79
4.6561-4.86780.31482970.30955732X-RAY DIFFRACTION82
4.8678-5.12420.31113270.30625999X-RAY DIFFRACTION87
5.1242-5.44490.31623850.31436414X-RAY DIFFRACTION93
5.4449-5.86480.33923370.32676792X-RAY DIFFRACTION97
5.8648-6.45390.35683790.31796864X-RAY DIFFRACTION99
6.4539-7.38530.31573420.30276933X-RAY DIFFRACTION99
7.3853-9.29510.26583550.24476965X-RAY DIFFRACTION99
9.2951-50.42690.28583830.26777008X-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)
11.35840.0403-0.13920.91480.12521.50380.0305-0.0349-0.0433-0.0366-0.05130.3408-0.0983-0.2139-01.5006-0.0042-0.0071.44370.09271.559342.011-43.149368.9673
20.70640.0699-0.47710.8322-0.04451.77480.0921-0.20610.06170.41810.01430.31070.0054-0.071201.5067-0.1038-0.03721.55430.04921.66743.9988-43.8232101.5206
31.2213-0.0237-0.96192.06940.16331.8123-0.0233-0.01710.3187-0.35370.03530.4449-0.5345-0.353801.5281-0.0516-0.45521.6560.02241.797230.0158-17.853662.6283
41.99850.1367-1.62220.1815-0.54794.3229-0.4284-0.4894-0.3818-0.04-0.1616-0.3421.48391.4891-0.46920.46760.2796-0.76072.66410.18721.958194.8903-54.024886.0494
50.6858-0.90480.28141.5069-0.60420.7210.17320.5806-0.581-1.02980.33331.11420.221-0.804402.9581-0.3298-0.22082.4073-0.01882.614915.763-88.56629.2302
60.67520.3852-0.26310.2301-0.11630.0963-0.62510.4357-0.8834-3.22060.5048-0.3162-0.5119-0.8071-0.00023.8137-0.1629-0.18112.69390.00642.777810.961-83.761215.9719
70.62620.09690.38140.21650.35640.5951-0.0140.06520.4426-0.30260.4126-1.0032-2.06961.48550.00011.773-0.27690.12112.8080.03812.174492.3904-13.22550.2137
80.4145-0.31920.32960.3337-0.33180.46110.41020.4140.1136-0.0424-0.06710.6927-1.3827-0.2790.00011.80720.0672-0.46981.77510.0761.836323.1663-23.26742.2332
91.4671.8831-0.0862.4288-0.03630.80390.24841.06680.1371-1.1093-0.7668-0.33910.32030.635502.1974-0.23330.17691.68830.04021.471449.3605-51.802937.4205
100.4632-0.3079-0.38671.55080.0350.4193-0.69040.4385-1.2506-0.60760.5981-0.6863-0.21240.2518-0.00011.1579-0.0954-0.00062.369-0.14532.211293.8774-52.950159.5472
110.2119-0.01170.19760.003-0.14770.46320.2641-0.4716-0.35111.9552-0.1298-0.69680.27611.9103-0.00191.3707-0.1128-0.38972.46240.22732.467784.1866-50.5138103.4581
121.2075-0.4980.16860.2910.2061.2464-0.8518-0.5955-1.0641.6919-0.21570.5550.65010.7433-0.07732.71720.2070.07591.920.35192.006162.1152-80.2832106.9701
130.05070.0104-0.0008-0.05830.04830.080.15450.72460.07440.4322-0.23730.3105-1.1804-0.8527-0.00012.663-0.0299-0.34132.42550.3313.69855.9985-29.75538.4801
141.243-0.0649-0.07751.14660.05681.6694-0.14580.1163-0.0888-0.14530.06940.4601-0.0785-0.2074-02.05890.04370.13931.47190.09781.626851.150744.103431.2622
150.6448-0.1564-0.13140.9156-0.36531.7850.04840.12920.0034-0.39250.03380.106-0.02930.133101.96290.00080.14511.55040.05511.673967.745344.77163.3394
160.4755-0.23270.37141.19860.38972.15480.03760.2293-0.1837-0.180.01240.39020.4456-0.2925-02.02860.01360.30881.70430.13692.240637.685318.695831.1825
170.54470.46410.3540.28870.1191.29880.0543-0.22080.27970.7414-0.1912-0.3979-0.5561.408302.1663-0.3107-0.02572.75990.20882.2654105.800655.181741.2259
180.91220.6306-0.20970.84740.26290.3396-0.4249-0.24830.2071.01520.48521.59760.0861-1.15670.00012.83950.30220.28212.64870.20942.82189.814289.436754.0602
190.3372-0.34470.18840.4734-0.41120.4294-0.6234-0.26130.65362.27820.86431.3859-0.3433-1.0966-0.00023.8140.20650.78622.68350.14053.7647-0.751684.495263.091
200.41410.3239-0.03490.35840.22540.2307-0.6299-0.7825-0.71230.16050.2245-0.66961.82630.9023-0.00012.63450.381-0.02672.59930.03752.069987.385414.159671.6405
210.79350.1484-0.21670.10080.10450.2881-0.0083-0.3188-0.4535-0.1129-0.31360.61490.6849-0.9921-0.00032.5864-0.10120.49071.8960.12132.278322.357224.054745.9926
221.0075-1.47730.71422.3242-1.32721.29630.1807-1.2728-0.4729-0.0626-0.7025-0.152-0.38010.1187-0.00012.63310.13830.33371.605-0.02511.366343.357552.694162.6558
230.41790.550.37990.60210.41230.4713-0.2232-0.22390.28411.0553-0.0942-0.3336-0.30970.0594-02.1513-0.0099-0.37212.33760.06592.184692.924753.955864.18
240.35290.20010.0580.14190.14050.1605-0.40550.64650.13830.3844-0.1885-0.569-0.3931.7861-0.00052.24450.0790.3962.55730.46312.5165104.179751.510120.8447
250.7390.1592-0.25420.1539-0.16830.1538-0.44020.1486-0.5563-1.29710.3479-0.6286-0.50510.1570.00022.7914-0.46140.43612.02140.13192.219186.208981.16596.9988
260.19430.0712-0.0167-0.01390.00360.0274-0.5995-0.1423-0.6814-1.07771.19411.2529-0.1-1.3291-0.00082.5776-0.46320.4042.90.21733.81325.202730.932842.277
270.03480.22510.18340.77850.46061.53550.1928-0.21781.64220.113-0.41590.3103-0.2731-0.292902.4403-0.07490.20183.1542-0.12573.314312.3379-26.636376.897
281.1491-0.3341-1.22990.5728-0.23551.57541.32190.76540.04010.3277-0.54481.06150.1105-0.3031-03.27430.3791-0.36512.9908-0.01183.744930.751829.411310.7368
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN BA
2X-RAY DIFFRACTION2CHAIN BB
3X-RAY DIFFRACTION3CHAIN BC
4X-RAY DIFFRACTION4CHAIN BD
5X-RAY DIFFRACTION5CHAIN BE
6X-RAY DIFFRACTION6CHAIN BF
7X-RAY DIFFRACTION7CHAIN BG
8X-RAY DIFFRACTION8CHAIN BH
9X-RAY DIFFRACTION9CHAIN BK
10X-RAY DIFFRACTION10CHAIN BL
11X-RAY DIFFRACTION11CHAIN BN
12X-RAY DIFFRACTION12CHAIN BP
13X-RAY DIFFRACTION13CHAIN BQ
14X-RAY DIFFRACTION14CHAIN AW
15X-RAY DIFFRACTION15CHAIN AR
16X-RAY DIFFRACTION16CHAIN AY
17X-RAY DIFFRACTION17CHAIN AS
18X-RAY DIFFRACTION18CHAIN AT
19X-RAY DIFFRACTION19CHAIN AU
20X-RAY DIFFRACTION20CHAIN AV
21X-RAY DIFFRACTION21CHAIN AZ
22X-RAY DIFFRACTION22CHAIN AI
23X-RAY DIFFRACTION23CHAIN AM
24X-RAY DIFFRACTION24CHAIN AO
25X-RAY DIFFRACTION25CHAIN AX
26X-RAY DIFFRACTION26CHAIN AJ
27X-RAY DIFFRACTION27CHAIN BC OR CHAIN AR
28X-RAY DIFFRACTION28CHAIN BD OR CHAIN AS

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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