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- PDB-2y0s: Crystal structure of Sulfolobus shibatae RNA polymerase in P21 sp... -

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基本情報

登録情報
データベース: PDB / ID: 2y0s
タイトルCrystal structure of Sulfolobus shibatae RNA polymerase in P21 space group
要素
  • (DNA-DIRECTED RNA ...) x 8
  • (RNA POLYMERASE SUBUNIT ...) x 5
キーワードTRANSFERASE / NUCLEOTIDYLTRANSFERASE / TRANSCRIPTION / METAL-BINDING
機能・相同性
機能・相同性情報


RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase activity / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : ...RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase activity / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / 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
Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G ...Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / 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 polymerase; domain 1 - #390 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo12 / Dihydrolipoamide Transferase / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain / RNA polymerase ii / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / Other non-globular / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Rubrerythrin, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Gyrase A; domain 2 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Homeodomain-like / HRDC-like superfamily / 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 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / : / 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, 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. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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. / Single Sheet / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Helix non-globular / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / Special / RNA polymerase Rpb6
類似検索 - ドメイン・相同性
FE3-S4 CLUSTER / 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 ...FE3-S4 CLUSTER / 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 (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.8 Å
データ登録者Wojtas, M. / Peralta, B. / Ondiviela, M. / Mogni, M. / Bell, S.D. / Abrescia, N.G.A.
引用
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.
#1: 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.
履歴
登録2010年12月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02011年2月16日Provider: repository / タイプ: Initial release
改定 1.12012年10月3日Group: Derived calculations / Version format compliance
改定 1.22019年1月30日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
改定 1.32019年10月30日Group: Data collection / Derived calculations / Other
カテゴリ: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
改定 1.42023年12月20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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.52024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" 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. THE SHEETS PRESENTED AS "BM" 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. THE SHEETS PRESENTED AS "RM" 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. THE SHEETS PRESENTED AS "WB" 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

ダウンロードとリンク

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集合体

登録構造単位
A: DNA-DIRECTED RNA POLYMERASE
B: DNA-DIRECTED RNA POLYMERASE
C: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
D: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
E: RNA POLYMERASE SUBUNIT 4
F: RNA POLYMERASE SUBUNIT 7
G: RNA POLYMERASE SUBUNIT 8
H: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
I: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
J: RNA POLYMERASE SUBUNIT 13
K: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
L: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
M: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
N: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
O: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
P: RNA POLYMERASE SUBUNIT 12
Q: RNA POLYMERASE SUBUNIT 13
R: DNA-DIRECTED RNA POLYMERASE
S: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
T: RNA POLYMERASE SUBUNIT 4
U: RNA POLYMERASE SUBUNIT 7
V: RNA POLYMERASE SUBUNIT 8
W: DNA-DIRECTED RNA POLYMERASE
X: RNA POLYMERASE SUBUNIT 12
Y: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
Z: 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)812,82544
ポリマ－811,26926
非ポリマー1,55618
水00
1
K: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
M: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
O: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
Q: RNA POLYMERASE SUBUNIT 13
R: DNA-DIRECTED RNA POLYMERASE
S: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
T: RNA POLYMERASE SUBUNIT 4
U: RNA POLYMERASE SUBUNIT 7
V: RNA POLYMERASE SUBUNIT 8
W: DNA-DIRECTED RNA POLYMERASE
X: RNA POLYMERASE SUBUNIT 12
Y: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
Z: 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)406,41222
ポリマ－405,63513
非ポリマー7789
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area61460 Å2
ΔGint-381.2 kcal/mol
Surface area173340 Å2
手法PISA
2
A: DNA-DIRECTED RNA POLYMERASE
B: DNA-DIRECTED RNA POLYMERASE
C: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
D: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
E: RNA POLYMERASE SUBUNIT 4
F: RNA POLYMERASE SUBUNIT 7
G: RNA POLYMERASE SUBUNIT 8
H: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
I: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
J: RNA POLYMERASE SUBUNIT 13
L: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
N: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
P: RNA POLYMERASE SUBUNIT 12
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)406,41222
ポリマ－405,63513
非ポリマー7789
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area63020 Å2
ΔGint-387.9 kcal/mol
Surface area180640 Å2
手法PISA
単位格子
Length a, b, c (Å)129.330, 195.909, 212.451
Angle α, β, γ (deg.)90.00, 105.73, 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

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 8:196 OR RESSEQ 202:507 OR RESSEQ...
211CHAIN R AND (RESSEQ 8:196 OR RESSEQ 202:507 OR RESSEQ...
112CHAIN A AND (RESSEQ 4:30 OR RESSEQ 45:151 OR RESSEQ 175:224 OR RESSEQ 233:879 ) AND (NOT ELEMENT H)
212CHAIN W AND (RESSEQ 4:30 OR RESSEQ 45:151 OR RESSEQ 175:224 OR RESSEQ 233:879 ) AND (NOT ELEMENT H)
113CHAIN C AND (RESSEQ 11:84 OR RESSEQ 102:395 ) AND (NOT ELEMENT H)
213CHAIN Y AND (RESSEQ 11:84 OR RESSEQ 102:395 ) AND (NOT ELEMENT H)
114CHAIN D AND (RESSEQ 2:85 OR RESSEQ 89:264 ) AND (NOT ELEMENT H)
214CHAIN S AND (RESSEQ 2:85 OR RESSEQ 89:264 ) AND (NOT ELEMENT H)
115CHAIN E AND (RESSEQ 1:151 OR RESSEQ 158:170 ) AND (NOT ELEMENT H)
215CHAIN T AND (RESSEQ 1:151 OR RESSEQ 158:170 ) AND (NOT ELEMENT H)
116CHAIN G AND (RESSEQ 7:116 ) AND (NOT ELEMENT H)
216CHAIN V AND (RESSEQ 7:116 ) AND (NOT ELEMENT H)
117CHAIN L AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
217CHAIN M AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
118CHAIN F AND (RESSEQ 3:92 ) AND (NOT ELEMENT H)
218CHAIN U AND (RESSEQ 3:92 ) AND (NOT ELEMENT H)
119CHAIN K AND (RESSEQ 11:92 ) AND (NOT ELEMENT H)
219CHAIN I AND (RESSEQ 11:92 ) AND (NOT ELEMENT H)
1110CHAIN H AND (RESSEQ 9:82 ) AND (NOT ELEMENT H)
2110CHAIN Z AND (RESSEQ 9:82 ) AND (NOT ELEMENT H)
1111CHAIN N AND (RESSEQ 1:64 ) AND (NOT ELEMENT H)
2111CHAIN O AND (RESSEQ 1:64 ) AND (NOT ELEMENT H)
1112CHAIN Q AND (RESSEQ 39:77 ) AND (NOT ELEMENT H)
2112CHAIN J AND (RESSEQ 39:77 ) AND (NOT ELEMENT H)
1113CHAIN P AND (RESSEQ 6:48 ) AND (NOT ELEMENT H)
2113CHAIN X AND (RESSEQ 6:48 ) 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

NCS oper: (Code: given
Matrix: (0.8546, -0.001801, 0.5193), (-0.002106, -1, -2.2E-5), (0.5193, -0.001092, -0.8546)
ベクター: -28.42, 0.6494, 102.3)

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要素

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DNA-DIRECTED RNA ... , 8種, 16分子 AWBRCYDSHZIKLMNO

#1: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB53, DNA-directed RNA polymerase
#2: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB55, DNA-directed RNA polymerase
#3: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB54, DNA-directed RNA polymerase
#4: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB56, DNA-directed RNA polymerase
#8: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB60, DNA-directed RNA polymerase
#9: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB61, DNA-directed RNA polymerase
#11: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB62, DNA-directed RNA polymerase
#12: 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 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB63, DNA-directed RNA polymerase

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RNA POLYMERASE SUBUNIT ... , 5種, 10分子 ETFUGVJQPX

#5: タンパク質 RNA POLYMERASE SUBUNIT 4


分子量: 20328.703 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB57, DNA-directed RNA polymerase
#6: タンパク質 RNA POLYMERASE SUBUNIT 7


分子量: 12822.612 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: RPO4 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB58
#7: タンパク質 RNA POLYMERASE SUBUNIT 8


分子量: 15139.458 Da / 分子数: 2 / Fragment: RPO8 / 由来タイプ: 天然 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB59
#10: タンパク質 RNA POLYMERASE SUBUNIT 13


分子量: 12169.592 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB65
#13: タンパク質・ペプチド RNA POLYMERASE SUBUNIT 12


分子量: 5606.951 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) SULFOLOBUS SHIBATAE (古細菌) / 参照: UniProt: B8YB64

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非ポリマー , 3種, 18分子

#14: 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
#15: 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
#16: 化合物 ChemComp-F3S / FE3-S4 CLUSTER


分子量: 295.795 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe3S4

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詳細

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: 3.45 Å3/Da / 溶媒含有率: 64.4 % / 解説: NONE
結晶化pH: 7.8 / 詳細: pH 7.8

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データ収集

回折
ID平均測定温度 (K)Crystal-ID
11101
21
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 X06DA11
シンクロトロンESRF ID14-120.9334
検出器
タイプID検出器日付
MARRESEARCH1CCD2009年11月6日
ADSC CCD2CCD
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
2Mx-ray1
放射波長
ID波長 (Å)相対比
111
20.93341
反射解像度: 3.79→50 Å / Num. obs: 100163 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / 冗長度: 7.2 % / Biso Wilson estimate: 79.35 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.1
反射 シェル解像度: 3.79→3.99 Å / 冗長度: 6.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 96.9

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解析

ソフトウェア
名称バージョン分類
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 2WAQ

2waq


解像度: 3.8→29.858 Å / SU ML: 0.55 / σ(F): 1.34 / 位相誤差: 36.85 / 立体化学のターゲット値: ML
詳細: DURING REFINEMENT IN PHENIX THE STRUCTURE-DIHEDRALS WERE RESTRAINED AGAINST THE 2WAQ. THE STATS PROVIDED INCLUDE THE RIDING HS DURING REFINEMENT THAT HAVE BEEN REMOVED FROM THE SUBMITTED ...詳細: DURING REFINEMENT IN PHENIX THE STRUCTURE-DIHEDRALS WERE RESTRAINED AGAINST THE 2WAQ. THE STATS PROVIDED INCLUDE THE RIDING HS DURING REFINEMENT THAT HAVE BEEN REMOVED FROM THE SUBMITTED COORDINATES TO FULFILL THE ATOMS LIMITATION OF 99999 OF THE PDB FORMAT.
Rfactor反射数%反射
Rfree0.3539 4959 5 %
Rwork0.2997 --
obs0.3024 99215 99.16 %
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 / Bsol: 71.911 Å2 / ksol: 0.35 e/Å3
原子変位パラメータBiso mean: 135.7 Å2
Baniso -1Baniso -2Baniso -3
1-17.0982 Å20 Å218.7796 Å2
2---6.959 Å2-0 Å2
3----10.1392 Å2
精密化ステップサイクル: LAST / 解像度: 3.8→29.858 Å
タンパク質核酸リガンド溶媒全体
原子数52442 0 30 0 52472
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01653497
X-RAY DIFFRACTIONf_angle_d1.51472248
X-RAY DIFFRACTIONf_dihedral_angle_d15.15820486
X-RAY DIFFRACTIONf_chiral_restr0.0788242
X-RAY DIFFRACTIONf_plane_restr0.0079242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11B8622X-RAY DIFFRACTIONPOSITIONAL
12R8622X-RAY DIFFRACTIONPOSITIONAL0.039
21A6620X-RAY DIFFRACTIONPOSITIONAL
22W6620X-RAY DIFFRACTIONPOSITIONAL0.059
31C2844X-RAY DIFFRACTIONPOSITIONAL
32Y2844X-RAY DIFFRACTIONPOSITIONAL0.035
41D2071X-RAY DIFFRACTIONPOSITIONAL
42S2071X-RAY DIFFRACTIONPOSITIONAL0.03
51E1298X-RAY DIFFRACTIONPOSITIONAL
52T1298X-RAY DIFFRACTIONPOSITIONAL0.031
61G878X-RAY DIFFRACTIONPOSITIONAL
62V878X-RAY DIFFRACTIONPOSITIONAL0.028
71L707X-RAY DIFFRACTIONPOSITIONAL
72M707X-RAY DIFFRACTIONPOSITIONAL0.031
81F701X-RAY DIFFRACTIONPOSITIONAL
82U701X-RAY DIFFRACTIONPOSITIONAL0.025
91K658X-RAY DIFFRACTIONPOSITIONAL
92I658X-RAY DIFFRACTIONPOSITIONAL0.04
101H609X-RAY DIFFRACTIONPOSITIONAL
102Z609X-RAY DIFFRACTIONPOSITIONAL0.034
111N514X-RAY DIFFRACTIONPOSITIONAL
112O514X-RAY DIFFRACTIONPOSITIONAL0.074
121Q332X-RAY DIFFRACTIONPOSITIONAL
122J332X-RAY DIFFRACTIONPOSITIONAL0.027
131P346X-RAY DIFFRACTIONPOSITIONAL
132X346X-RAY DIFFRACTIONPOSITIONAL0.032
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.84310.38011500.34133030X-RAY DIFFRACTION96
3.8431-3.88820.43071650.37682993X-RAY DIFFRACTION96
3.8882-3.93550.45741780.41993052X-RAY DIFFRACTION96
3.9355-3.98520.35181430.33873059X-RAY DIFFRACTION97
3.9852-4.03760.35211550.30293113X-RAY DIFFRACTION97
4.0376-4.09270.31611650.30133107X-RAY DIFFRACTION99
4.0927-4.15110.36451720.29713064X-RAY DIFFRACTION99
4.1511-4.21280.38331550.28763161X-RAY DIFFRACTION99
4.2128-4.27850.33671640.28563141X-RAY DIFFRACTION99
4.2785-4.34840.31831670.27823161X-RAY DIFFRACTION100
4.3484-4.42320.30851750.26823151X-RAY DIFFRACTION100
4.4232-4.50330.32231700.26613135X-RAY DIFFRACTION100
4.5033-4.58970.32721630.26713152X-RAY DIFFRACTION100
4.5897-4.6830.31631800.25343155X-RAY DIFFRACTION100
4.683-4.78440.29561850.2663148X-RAY DIFFRACTION100
4.7844-4.89520.33071350.27863184X-RAY DIFFRACTION100
4.8952-5.01710.36051650.28663146X-RAY DIFFRACTION100
5.0171-5.15210.3191580.2993180X-RAY DIFFRACTION100
5.1521-5.30290.38391560.30033174X-RAY DIFFRACTION100
5.3029-5.4730.381740.32293140X-RAY DIFFRACTION100
5.473-5.66740.40821630.33183182X-RAY DIFFRACTION100
5.6674-5.89260.41111590.33733214X-RAY DIFFRACTION100
5.8926-6.15860.42121680.33623165X-RAY DIFFRACTION100
6.1586-6.48020.39391710.33433149X-RAY DIFFRACTION100
6.4802-6.88150.37631560.32173185X-RAY DIFFRACTION100
6.8815-7.40530.3921700.29483147X-RAY DIFFRACTION100
7.4053-8.13690.34451700.27473216X-RAY DIFFRACTION100
8.1369-9.28320.30591690.25973187X-RAY DIFFRACTION100
9.2832-11.58120.29891750.24993171X-RAY DIFFRACTION99
11.5812-29.85860.37731830.34873192X-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)
1-0.14760.135-0.06510.2786-0.07440.1401-0.1551-0.2376-0.0443-0.5163-0.2172-0.07750.0853-0.0038-0.2167-0.05070.0977-0.040.8134-0.05881.01332.4017-57.888432.3977
2-0.1961-0.0311-0.18230.10690.02740.1629-0.05620.1026-0.08570.12680.0227-0.1706-0.0767-0.20150.00370.17250.04750.01290.3809-0.0690.4183-22.409-37.496236.8474
30.1490.2041-0.3222-0.0811-0.4555-0.0342-0.0168-0.05050.0193-0.0162-0.02710.0686-0.10.1548-0.08210.3726-0.0455-0.05270.3661-0.22370.2518-6.8477-25.831832.1707
40.1485-0.22170.1466-0.29240.06680.12660.1194-0.29760.2606-0.3735-0.06020.02710.2524-0.01960.00060.7340.06980.04240.4240.01590.3067-0.463-52.6675-15.6053
50.0001-0.0840.00940.11070.05450.06720.12830.0319-0.24360.0557-0.08440.0811-0.17820.0593-00.4223-0.16190.36940.8282-0.05441.252728.7579-23.9903-4.395
6-0.1287-0.01050.05490.07110.123-0.00440.1039-0.1342-0.0704-0.1319-0.0496-0.108-0.0563-0.11150.00260.32210.0188-0.01080.3610.02980.4382-9.2768-45.4227.6881
70.51720.3764-0.29990.3983-0.10350.130.0160.1207-0.51580.1642-0.295-0.528-0.4017-0.2986-0.27470.4084-0.0422-0.31250.4315-0.04830.2106-7.55-22.030157.0288
80.159-0.1669-0.0660.22380.2770.2626-0.12990.1895-0.56120.0942-0.31850.102-0.313-0.0299-0.25460.4114-0.1009-0.28440.090.27410.560325.05722.01622.4028
90.03290.46410.15170.35970.19530.10650.03810.074-0.17080.16330.02290.0325-0.2560.09220.01360.2782-0.109-0.03910.26690.02910.648510.5528-32.558446.1699
10-0.0013-0.1817-0.1290.00810.0930.2316-0.1357-0.10960.3037-0.21090.34960.04380.69140.2207-0.05010.1018-0.3362-0.24260.9945-0.19420.7493-48.7444-63.705612.5161
11-0.2158-0.2317-0.29390.498-0.34920.96390.1760.3103-0.35760.388-0.4526-0.5204-0.4988-0.7549-0.08820.0590.2285-0.07331.41220.11861.0985-58.1954-37.38923.2417
120.0706-0.1121-0.0821-0.0039-0.02810.15250.23720.45430.03420.6133-0.0303-0.10020.135-0.211301.23420.2846-0.12510.83010.23370.70327.2662-73.592771.7878
13-0.0126-0.01380.00260.00190.04690.0936-0.2078-0.2689-0.1595-0.2132-0.2663-0.0265-0.0593-0.078900.99150.1794-0.31520.6979-0.09871.663934.9094-99.109275.2421
140.0527-0.0394-0.04410.0066-0.00420.0055-0.0970.08780.12960.1137-0.19770.19260.06240.1738-01.1860.4046-0.09570.8918-0.02171.027616.016-85.40981.7414
150.03140.00530.0240.01230.0066-0.0039-0.28120.2126-0.12210.19290.10210.1625-0.17550.207701.27040.5805-0.64011.4729-0.22231.545132.742-81.331690.2316
160.33270.15250.44840.07150.17671.453-0.4086-0.1078-0.4628-0.18970.01420.0709-0.67570.116-0.12190.45530.64470.20911.04570.02030.8664-50.8306-12.469951.86
170.0452-0.044-0.04340.06050.04760.0442-0.0323-0.553-0.1271-0.5671-0.0430.138-0.17710.140700.81990.0432-0.09730.630.10850.551616.0118-23.429661.2122
180.70420.04510.08070.5320.2391-0.1549-0.15960.62080.27230.61560.5526-0.11040.31120.04980.22980.64010.16210.01430.32520.17490.1555-9.6494-50.932365.2257
190.4205-0.04410.2637-0.1448-0.09680.0338-1.15870.1071-0.04330.516-0.0490.2573-0.11910.2618-0.3518-0.0239-0.18450.04081.12990.06391.0356-52.4435-51.924143.0054
20-0.0184-0.1141-0.11830.2934-0.1840.14240.2460.12820.05930.3630.72630.1905-0.9-0.49240.8549-0.2559-0.4373-0.60290.9344-0.34250.5524-41.7889-49.2568-0.0932
210.1247-0.11070.16670.0533-0.08780.13720.0424-0.5694-0.3504-0.75920.0349-0.0322-0.2073-0.1858-00.8962-0.0762-0.07610.8229-0.320.9492-20.1672-78.9961-3.2582
22-0.0105-0.0121-0.0162-0.00150.0087-0.0005-0.1563-0.1766-0.172-0.104-0.0838-0.1586-0.1032-0.103-00.78450.2912-0.71021.1375-0.15461.696532.0157-31.475567.3982
230.11280.1426-0.02250.1187-0.11880.0124-0.10750.1643-0.28660.2203-0.10980.1626-0.20140.192601.22450.0241-0.11351.0783-0.09691.143415.900958.50891.2333
24-0.23630.0703-0.04690.17970.07910.2848-0.0960.0102-0.08320.0002-0.0031-0.304-0.108-0.334-0.00010.8832-0.06790.05240.4722-0.09250.3812-28.765338.212359.0944
25-0.03720.11480.02830.0726-0.36140.13020.0159-0.0955-0.2161-0.0433-0.1042-0.0837-0.1882-0.029601.10950.02530.19980.652-0.13220.682-17.88926.523971.1429
260.20240.3368-0.1538-0.19750.10780.14430.19270.13280.04830.23330.0095-0.00050.0791-0.109300.92850.02280.1470.6664-0.0570.5766-37.356953.3594115.3252
270.05660.0686-0.03850.09780.10630.0645-0.46-0.06680.2195-0.0628-0.0585-0.01450.2410.0271-0.00081.03250.2452-0.40810.59920.13830.8233-6.638424.6143120.9662
28-0.1351-0.0818-0.22860.03040.22730.10680.02270.10070.09280.1094-0.0758-0.14210.0605-0.1433-00.9405-0.02690.00790.64010.04680.654-32.758746.11790.8481
290.2345-0.13790.1550.12730.08740.1175-0.1770.16220.16220.1313-0.1717-0.24230.3361-0.11601.11260.00310.46320.703-0.05211.0446-5.595722.730449.5813
300.02490.0132-0.02740.03060.24850.1252-0.198-0.11590.0456-0.0802-0.27310.06910.00320.019800.68330.04480.21270.36120.39961.12584.2811-1.316596.1059
310.2062-0.37090.05830.2062-0.1014-0.0907-0.1776-0.05820.0501-0.05570.0467-0.07420.0803-0.011901.03380.05460.06250.29110.0560.81114.309933.236768.2339
320.09850.06530.0201-0.02330.0408-0.02820.0108-0.0228-0.1011-0.04220.5174-0.0987-0.1779-0.1745-01.00930.3953-0.12841.2193-0.06110.7319-63.885864.485666.2799
33-0.05020.0354-0.01830.0504-0.036-0.06910.06190.1725-0.24040.1113-0.8243-0.6553-0.2239-0.7962-0.00020.9283-0.1319-0.32351.6201-0.11180.7485-66.497638.204852.1582
340.01890.03320.0422-0.02-0.05560.09410.05950.0750.28510.01630.0187-0.05460.3034-0.051801.4226-0.32330.44880.681-0.01020.713214.797674.275644.5818
350.0358-0.014-0.0577-0.00640.02440.0749-0.16330.20890.17920.0725-0.4374-0.00960.05220.064200.9726-0.0878-0.30321.0536-0.07361.769540.348399.66155.9795
36-0.01480.01680.00270.03050.05540.04640.2243-0.21950.188-0.203-0.07410.27770.24460.2901-01.6324-0.30190.01691.11-0.14551.538927.542186.008340.569
370.02860.01270.00190.00140.0019-0.006-0.2086-0.1856-0.0595-0.09180.05830.0498-0.04490.046501.1801-0.42240.2831.7881-0.44242.073746.23381.851841.9229
380.1145-0.117-0.01380.1102-0.11840.0807-0.50540.2637-0.03070.1504-0.19270.07630.02090.053901.0734-0.4712-0.07741.1488-0.21510.6411-45.315613.229331.5281
390.0943-0.02020.05470.03480.04750.0616-0.01830.0723-0.03980.0704-0.13890.3887-0.06150.409701.1482-0.03960.31350.95540.11051.076216.759124.04658.1777
400.16370.04240.14860.05920.05750.01270.2974-0.3693-0.4126-0.40850.1948-0.1724-0.4418-0.15730.00011.2715-0.1950.27240.36760.04350.4983-3.141851.59541.4703
410.0043-0.0267-0.0090.0492-0.11280.0598-0.3343-0.3148-0.1263-0.3465-0.12790.2224-0.28050.229901.5110.141-0.30721.39220.22260.7437-51.250252.626538.2357
42-0.06110.04920.04560.00370.14630.1392-0.8492-0.1880.1037-0.0906-0.1406-0.12260.1932-0.1194-0.00690.73180.3798-0.12971.5675-0.29561.1841-64.511949.986880.626
430.17580.0221-0.07850.05960.01970.0404-0.11410.27890.18640.2773-0.09850.3030.01340.107301.44550.33950.06670.8489-0.16570.9675-47.603479.689294.5481
44-0.01460.01870.01310.00760.0021-0.0003-0.0505-0.0248-0.1516-0.01150.1156-0.0961-0.017-0.011500.64490.05510.27931.4101-0.25772.272633.766732.160361.1061
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 4:298
2X-RAY DIFFRACTION2CHAIN A AND RESID 299:755
3X-RAY DIFFRACTION3CHAIN A AND RESID 756:879
4X-RAY DIFFRACTION4CHAIN B AND RESID 8:174
5X-RAY DIFFRACTION5CHAIN B AND RESID 175:334
6X-RAY DIFFRACTION6CHAIN B AND RESID 335:1122
7X-RAY DIFFRACTION7CHAIN C AND RESID 11:125
8X-RAY DIFFRACTION8CHAIN C AND RESID 126:249
9X-RAY DIFFRACTION9CHAIN C AND RESID 250:395
10X-RAY DIFFRACTION10CHAIN D AND RESID 2:157
11X-RAY DIFFRACTION11CHAIN D AND RESID 158:264
12X-RAY DIFFRACTION12CHAIN E AND RESID 1:78
13X-RAY DIFFRACTION13CHAIN E AND RESID 79:177
14X-RAY DIFFRACTION14CHAIN F AND RESID 3:46
15X-RAY DIFFRACTION15CHAIN F AND RESID 47:92
16X-RAY DIFFRACTION16CHAIN G
17X-RAY DIFFRACTION17CHAIN H
18X-RAY DIFFRACTION18CHAIN K
19X-RAY DIFFRACTION19CHAIN L
20X-RAY DIFFRACTION20CHAIN N AND RESID 1:64
21X-RAY DIFFRACTION21CHAIN P AND RESID 4:48
22X-RAY DIFFRACTION22CHAIN Q
23X-RAY DIFFRACTION23CHAIN W AND RESID 4:298
24X-RAY DIFFRACTION24CHAIN W AND RESID 299:755
25X-RAY DIFFRACTION25CHAIN W AND RESID 756:879
26X-RAY DIFFRACTION26CHAIN R AND RESID 8:174
27X-RAY DIFFRACTION27CHAIN R AND RESID 175:334
28X-RAY DIFFRACTION28CHAIN R AND RESID 335:1122
29X-RAY DIFFRACTION29CHAIN Y AND RESID 11:125
30X-RAY DIFFRACTION30CHAIN Y AND RESID 126:249
31X-RAY DIFFRACTION31CHAIN Y AND RESID 250:395
32X-RAY DIFFRACTION32CHAIN S AND RESID 2:157
33X-RAY DIFFRACTION33CHAIN S AND RESID 158:264
34X-RAY DIFFRACTION34CHAIN T AND RESID 1:78
35X-RAY DIFFRACTION35CHAIN T AND RESID 79:177
36X-RAY DIFFRACTION36CHAIN U AND RESID 3:46
37X-RAY DIFFRACTION37CHAIN U AND RESID 47:92
38X-RAY DIFFRACTION38CHAIN V
39X-RAY DIFFRACTION39CHAIN Z
40X-RAY DIFFRACTION40CHAIN I
41X-RAY DIFFRACTION41CHAIN M
42X-RAY DIFFRACTION42CHAIN O AND RESID 1:64
43X-RAY DIFFRACTION43CHAIN X AND RESID 4:48
44X-RAY DIFFRACTION44CHAIN J

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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://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