[日本語] English
万見
- PDB-4c3j: Structure of 14-subunit RNA polymerase I at 3.35 A resolution, cr... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4c3j
タイトルStructure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90
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 ...) x 5
キーワードTRANSCRIPTION
機能・相同性
機能・相同性情報


nuclear DNA-directed RNA polymerase complex / 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 / 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 ...nuclear DNA-directed RNA polymerase complex / 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 / 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 / regulation of cell size / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
類似検索 - 分子機能
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / : / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / : / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / Pol I subunit A12, C-terminal zinc ribbon / 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 / : / RNA polymerase I, Rpa2 specific domain / 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 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 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / 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 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, RBP11-like subunit / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Gyrase A; domain 2 / Homeodomain-like / 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 M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / 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 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, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / 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 / Zinc finger, TFIIS-type / 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 / 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 / Nucleic acid-binding proteins / Helix non-globular / Beta Complex / Special / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6
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 / 分子置換 / 解像度: 3.35 Å
データ登録者Fernandez-Tornero, C. / Moreno-Morcillo, M. / Rashid, U.J. / Taylor, N.M.I. / Ruiz, F.M. / Gruene, T. / Legrand, P. / Steuerwald, U. / Muller, C.W.
引用ジャーナル: Nature / 年: 2013
タイトル: Crystal Structure of the 14-Subunit RNA Polymerase I
著者: Fernandez-Tornero, C. / Moreno-Morcillo, M. / Rashid, U.J. / Taylor, N.M.I. / Ruiz, F.M. / Gruene, T. / Legrand, P. / Steuerwald, U. / Muller, C.W.
履歴
登録2013年8月24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 1.22024年5月8日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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

-
集合体

登録構造単位
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 RPABC1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)590,72221
ポリマ－590,26514
非ポリマー4587
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area95850 Å2
ΔGint-524.1 kcal/mol
Surface area214800 Å2
手法PISA
単位格子
Length a, b, c (Å)401.020, 139.840, 140.940
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number5
Space group name H-MC121

-
要素

-
DNA-DIRECTED RNA POLYMERASE I SUBUNIT ... , 7種, 7分子 ABDGIMN

#1: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190 / DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DN A-DIRECTED RNA POLYMERASE I LARGEST ...DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DN A-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT / DNA-DIRECTED RNA POLY MERASE I SUBUNIT A190


分子量: 186676.969 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P10964, DNA-directed RNA polymerase
#2: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 / DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DN A-DIRECTED RNA POLYMERASE I ...DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DN A-DIRECTED RNA POLYMERASE I POLYPEPTIDE 2 / RNA POLYMERASE I SUBUNIT 2 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A135


分子量: 135910.328 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P22138, DNA-directed RNA polymerase
#4: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14 / A14 / DNA-DIRECTED RNA POLYMERASE I 14 KDA POLYPEPTIDE / DNA- DIRECTED RNA POLYMERASE I SUBUNIT A14


分子量: 14585.103 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P50106, DNA-directed RNA polymerase
#7: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 / A43 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 36 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A43


分子量: 36264.852 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P46669, DNA-directed RNA polymerase
#9: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 / A12 / A12.2 / DNA-DIRECTED RNA POLYMERASE I 13.7 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A12.2


分子量: 13676.566 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P32529, DNA-directed RNA polymerase
#13: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 / A49 / DNA-DIRECTED RNA POLYMERASE I 49 KDA POLYPEPTIDE / DNA- DIRECTED RNA POLYMERASE I SUBUNIT A49


分子量: 46721.707 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: Q01080, DNA-directed RNA polymerase
#14: タンパク質 DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 / A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POL YPEPTIDE / A34.5 / DNA-DIRECTED RNA ...A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POL YPEPTIDE / A34.5 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A34.5


分子量: 26933.518 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P47006, DNA-directed RNA polymerase

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

#3: 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 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT AC40


分子量: 37732.613 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P07703, DNA-directed RNA polymerase
#11: タンパク質 DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2 / RNA POLYMERASES I AND III SUBUNIT AC2 / AC19 / DNA-DIRECTED RNA POLYMERASES I AND III 16 KDA ...RNA POLYMERASES I AND III SUBUNIT AC2 / AC19 / DNA-DIRECTED RNA POLYMERASES I AND III 16 KDA POLYPEPTIDE / RPA19 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT AC19


分子量: 16167.860 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P28000, DNA-directed RNA polymerase

-
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ... , 5種, 5分子 EFHJL

#5: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / DNA-DIREC TED RNA POLYMERASE I SUBUNIT ABC27


分子量: 25117.094 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P20434, DNA-directed RNA polymerase
#6: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIR ECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIR ECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / DNA-DIREC TED RNA POLYMERASE I SUBUNIT ABC23


分子量: 17931.834 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P20435, DNA-directed RNA polymerase
#8: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPE DE / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ABC14.5


分子量: 16525.363 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P20436, DNA-directed RNA polymerase
#10: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTID E / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ABC10-BETA


分子量: 8290.732 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P22139, DNA-directed RNA polymerase
#12: タンパク質 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ...RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ABC10-ALPHA


分子量: 7729.969 Da / 分子数: 1 / 由来タイプ: 天然
詳細: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: SC1613 / 参照: UniProt: P40422, DNA-directed RNA polymerase

-
非ポリマー , 1種, 7分子

#15: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Zn

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.35 Å3/Da / 溶媒含有率: 65 % / 解説: NONE
結晶化詳細: 10% MPD, 0.1M TRIS HCL, PH 7.5

-
データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.98011
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年12月2日 / 詳細: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
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: 0.98011 Å / 相対比: 1
反射解像度: 3.35→80 Å / Num. obs: 112047 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 7.7 % / Biso Wilson estimate: 124.28 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.48
反射 シェル解像度: 3.35→3.44 Å / 冗長度: 7.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.87 / % possible all: 100

-
解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
SHARP位相決定
BUSTER2.11.5精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.35→49.05 Å / Cor.coef. Fo:Fc: 0.9242 / Cor.coef. Fo:Fc free: 0.9167 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
Rfactor反射数%反射Selection details
Rfree0.2204 5612 5.03 %RANDOM
Rwork0.213 ---
obs0.2134 111523 99.55 %-
原子変位パラメータBiso mean: 135.05 Å2
Baniso -1Baniso -2Baniso -3
1--6.8397 Å20 Å2-11.5457 Å2
2--13.4772 Å20 Å2
3----6.6376 Å2
Refine analyzeLuzzati coordinate error obs: 0.888 Å
精密化ステップサイクル: LAST / 解像度: 3.35→49.05 Å
タンパク質核酸リガンド溶媒全体
原子数34545 0 7 0 34552
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00835202HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9647550HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d16642SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes952HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5008HARMONIC5
X-RAY DIFFRACTIONt_it35202HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion3.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4611SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39731SEMIHARMONIC4
LS精密化 シェル解像度: 3.35→3.44 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2692 399 5.09 %
Rwork0.2565 7441 -
all0.2571 7840 -
obs--99.55 %
精密化 TLS手法: refined / Origin x: -53.3901 Å / Origin y: -68.0187 Å / Origin z: 69.7886 Å
111213212223313233
T0.2746 Å20.0617 Å20.1518 Å2-0.1117 Å20.025 Å2--0.306 Å2
L0.6904 °20.0397 °20.0799 °2-0.6157 °20.0336 °2--0.8223 °2
S-0.0195 Å °0.0743 Å °0.0347 Å °-0.1073 Å °0.0388 Å °-0.1914 Å °-0.0103 Å °-0.0695 Å °-0.0193 Å °
精密化 TLSグループSelection details: { *|* }

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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