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- PDB-4c3h: Structure of 14-subunit RNA polymerase I at 3.27 A resolution, cr... -

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基本情報

登録情報
データベース: PDB / ID: 4c3h
タイトルStructure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93
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
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 / 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 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / regulation of cell size / 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 / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / Dual incision in TC-NER / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / 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 / mitochondrion / 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. / 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 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 / Nucleic acid-binding proteins / Helix non-globular / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / Special / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase 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: 3.27 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-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 -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-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
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
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
  • 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 area88630 Å2
ΔGint-520.3 kcal/mol
Surface area215820 Å2
手法PQS
単位格子
Length a, b, c (Å)425.240, 140.620, 139.720
Angle α, β, γ (deg.)90.00, 93.35, 90.00
Int Tables number5
Space group name H-MC121

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要素

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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 / DNA-DIRECTED RNA POLYMERASE I LARGEST ...DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT / DNA-DIRECTED RNA POLYMERASE 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 / 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 / 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
#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
#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
#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
#14: 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 / DNA-DIRECTED RNA ...A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POLYPEPTIDE / 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

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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 RNA POLYMERASES I AND III 40 KDA ...RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RNA 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
#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

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

#5: 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\ / ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 27 KDA POLYPEPTIDE / DNA-DIRECTED 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
#6: 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 / DNA-DIRECTED 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
#8: 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 / 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
#10: 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 / AB C8 / DNA-DIRECTED RNA POLYMERASES ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 8.3 KDA POLYPEPTIDE / 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
#12: 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 / DNA-DIRECTED RNA POLYMERASE I ...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

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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

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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: 3.53 Å3/Da / 溶媒含有率: 0.67 % / 解説: NONE
結晶化詳細: 24% ETHYLENGLYCOL, 0.1M MES PH 6.8

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 1 / 波長: 1.0716
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年6月8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: 1.0716 Å / 相対比: 1
反射解像度: 3.27→97.3 Å / Num. obs: 127066 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 10.9 % / Biso Wilson estimate: 155.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.85
反射 シェル解像度: 3.27→3.35 Å / 冗長度: 11.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.51 / % possible all: 99.9

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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: 3.27→47.88 Å / Cor.coef. Fo:Fc: 0.9358 / Cor.coef. Fo:Fc free: 0.9379 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.375
Rfactor反射数%反射Selection details
Rfree0.2257 6209 5 %RANDOM
Rwork0.2205 ---
obs0.2208 124088 97.66 %-
原子変位パラメータBiso mean: 171.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.781 Å20 Å210.4002 Å2
2--23.2443 Å20 Å2
3----26.0253 Å2
Refine analyzeLuzzati coordinate error obs: 1.05 Å
精密化ステップサイクル: LAST / 解像度: 3.27→47.88 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_d0.00835201HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9647547HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d16641SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes952HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5007HARMONIC5
X-RAY DIFFRACTIONt_it35201HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion3.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4610SEMIHARMONIC5
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_contact39371SEMIHARMONIC4
LS精密化 シェル解像度: 3.27→3.35 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.3141 341 5.11 %
Rwork0.309 6335 -
all0.3093 6676 -
obs--97.66 %
精密化 TLS手法: refined / Origin x: 53.2647 Å / Origin y: -2.2886 Å / Origin z: 2.8283 Å
111213212223313233
T0.3036 Å20.124 Å2-0.152 Å2--0.088 Å2-0.0243 Å2--0.2862 Å2
L1.1727 °20.0312 °2-0.0403 °2-0.9537 °2-0.2713 °2--1.1218 °2
S0.0107 Å °0.0864 Å °0.0099 Å °-0.1496 Å °0.0072 Å °0.2416 Å °0.1551 Å °0.1204 Å °-0.0178 Å °
精密化 TLSグループSelection details: ALL

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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。
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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。
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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

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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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