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- PDB-4bbs: Structure of an initially transcribing RNA polymerase II-TFIIB complex -

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基本情報

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データベース: PDB / ID: 4bbs
タイトルStructure of an initially transcribing RNA polymerase II-TFIIB complex
要素
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...) x 5
  • 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3'
  • 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3'
  • 5'-R(*AP*UP*AP*UP*CP*AP)-3'
  • TRANSCRIPTION INITIATION FACTOR IIB
キーワードTRANSCRIPTION
機能・相同性
機能・相同性情報


RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / 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 ...RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / 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 / termination of RNA polymerase II transcription / 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 general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / : / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / 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 / RNA polymerase II complex binding / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / Dual incision in TC-NER / transcription by RNA polymerase III / translesion synthesis / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / tRNA transcription by RNA polymerase III / translation initiation factor binding / TBP-class protein binding / : / : / : / : / : / : / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / P-body / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / mRNA processing / cytoplasmic stress granule / peroxisome / ribosome biogenesis / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
類似検索 - 分子機能
Cyclin A; domain 1 - #170 / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal 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 ...Cyclin A; domain 1 - #170 / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal 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 / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / N-terminal domain of TfIIb - #10 / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Zinc finger, TFIIB-type / RNA polymerase II, Rpb2 subunit, wall domain / TFIIB zinc-binding / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / Growth Hormone; Chain: A; / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Gyrase A; domain 2 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like superfamily / Homeodomain-like / Zinc finger TFIIS-type signature. / 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, 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. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
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: 3.6 Å
データ登録者Sainsbury, S. / Niesser, J. / Cramer, P.
引用ジャーナル: Nature / 年: 2013
タイトル: Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
著者: Sainsbury, S. / Niesser, J. / Cramer, P.
履歴
登録2012年9月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02012年11月14日Provider: repository / タイプ: Initial release
改定 1.12013年1月30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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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 "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 12-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 12-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 II SUBUNIT RPB1
B: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
C: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
D: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
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 II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: TRANSCRIPTION INITIATION FACTOR IIB
N: 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3'
P: 5'-R(*AP*UP*AP*UP*CP*AP)-3'
T: 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)567,50627
ポリマ－566,86916
非ポリマー63711
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 area87400 Å2
ΔGint-441 kcal/mol
Surface area197180 Å2
手法PQS
単位格子
Length a, b, c (Å)222.170, 386.010, 254.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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要素

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DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 7種, 7分子 ABCDGIK

#1: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE II SUBUNIT B220 / RPB1


分子量: 191821.578 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P04050, DNA-directed RNA polymerase
#2: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / RNA POLYMERASE II SUBUNIT 2 / B150 / RPB2 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


分子量: 138937.297 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P08518, DNA-directed RNA polymerase
#3: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II ...RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / RPB3


分子量: 35330.457 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P16370
#4: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / RNA POLYMERASE II SUBUNIT B4 / B32 / RPB4 / DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE


分子量: 25451.191 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P20433
#7: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / RNA POLYMERASE II SUBUNIT B7 / B16 / RPB7


分子量: 19081.053 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P34087
#9: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / RNA POLYMERASE II SUBUNIT B9 / B12.6 / RPB9 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / ...RNA POLYMERASE II SUBUNIT B9 / B12.6 / RPB9 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9


分子量: 14308.161 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P27999
#11: タンパク質 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / RNA POLYMERASE II SUBUNIT B11 / B13.6 / RPB11 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE


分子量: 13633.493 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P38902

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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 / RPB5 / DNA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / RPB5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE


分子量: 25117.094 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 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 / RPB6 / DNA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / RPB6 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE


分子量: 17931.834 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 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 / RPB8 / DNA-DIRECTED RNA ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / RPB8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE


分子量: 16525.363 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 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 / ABC8 / RPB10 / DNA-DIRECTED RNA ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / RPB10 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTIDE


分子量: 8290.732 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 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 / RPB12


分子量: 7729.969 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P40422

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DNA鎖 , 2種, 2分子 NT

#14: DNA鎖 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3' / NON-TEMPLATE DNA


分子量: 4265.781 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SACCHAROMYCES CEREVISIAE (パン酵母)
#16: DNA鎖 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3' / TEMPLATE DNA


分子量: 8327.377 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SACCHAROMYCES CEREVISIAE (パン酵母)

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タンパク質 / RNA鎖 , 2種, 2分子 MP

#13: タンパク質 TRANSCRIPTION INITIATION FACTOR IIB / GENERAL TRANSCRIPTION FACTOR TFIIB / TRANSCRIPTION FACTOR E / TFIIB


分子量: 38257.340 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母)
発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P29055
#15: RNA鎖 5'-R(*AP*UP*AP*UP*CP*AP)-3' / RNA PRODUCT


分子量: 1860.173 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SACCHAROMYCES CEREVISIAE (パン酵母)

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非ポリマー , 2種, 11分子

#17: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 9 / 由来タイプ: 合成 / 式: Zn
#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

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試料調製

結晶マシュー密度: 5.83 Å3/Da / 溶媒含有率: 78.74 % / 解説: NONE

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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: SLS / ビームライン: X06SA / 波長: 0.9188
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9188 Å / 相対比: 1
反射解像度: 3.6→50 Å / Num. obs: 126022 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / 冗長度: 7.5 % / Biso Wilson estimate: 86.97 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 9.5

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解析

ソフトウェア名称: PHENIX / バージョン: (PHENIX.REFINE) / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.6→49.273 Å / SU ML: 0.44 / σ(F): 1.99 / 位相誤差: 22.21 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.225 2519 2 %
Rwork0.1847 --
obs0.1855 125981 99.95 %
溶媒の処理減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 81.817 Å2 / ksol: 0.326 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--8.364 Å20 Å20 Å2
2---0.8756 Å20 Å2
3----12.6202 Å2
精密化ステップサイクル: LAST / 解像度: 3.6→49.273 Å
タンパク質核酸リガンド溶媒全体
原子数32797 612 11 0 33420
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00834125
X-RAY DIFFRACTIONf_angle_d1.1246123
X-RAY DIFFRACTIONf_dihedral_angle_d17.62112962
X-RAY DIFFRACTIONf_chiral_restr0.0755202
X-RAY DIFFRACTIONf_plane_restr0.0045884
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5999-3.66920.3431400.29826800X-RAY DIFFRACTION100
3.6692-3.7440.30541360.27696784X-RAY DIFFRACTION100
3.744-3.82540.30851390.26066802X-RAY DIFFRACTION100
3.8254-3.91440.28581420.24976819X-RAY DIFFRACTION100
3.9144-4.01220.28421370.23316813X-RAY DIFFRACTION100
4.0122-4.12060.2381400.20896834X-RAY DIFFRACTION100
4.1206-4.24180.24271380.18796773X-RAY DIFFRACTION100
4.2418-4.37870.2161400.16926845X-RAY DIFFRACTION100
4.3787-4.5350.19511370.14776826X-RAY DIFFRACTION100
4.535-4.71650.16461420.14216833X-RAY DIFFRACTION100
4.7165-4.9310.17581380.14336835X-RAY DIFFRACTION100
4.931-5.19070.20411410.15556874X-RAY DIFFRACTION100
5.1907-5.51550.2091400.16816835X-RAY DIFFRACTION100
5.5155-5.94070.22541400.18086884X-RAY DIFFRACTION100
5.9407-6.53730.23781400.18776898X-RAY DIFFRACTION100
6.5373-7.48040.20851410.1676899X-RAY DIFFRACTION100
7.4804-9.41380.19521420.14146985X-RAY DIFFRACTION100
9.4138-49.27780.2111460.19377123X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3505-0.06820.17080.32990.0251.03150.06720.2380.1886-0.0573-0.1612-0.0135-0.04230.0251-0.06130.093-0.03340.01320.04960.04080.19660.997648.2421-2.381
20.9506-0.20640.20310.3123-0.15940.3008-0.02640.00690.46340.0485-0.0585-0.0717-0.15720.0159-0.00030.4788-0.03630.01960.34930.10230.69515.996475.5888-2.1138
30.6034-0.42140.22680.7532-0.24970.4114-0.0017-0.04050.091-0.14560.05410.3191-0.0658-0.31490.010.43090.0689-0.0460.5386-0.00370.5468-29.167751.348317.9126
41.8365-0.52781.48081.99980.78651.9440.14810.40930.1026-0.04890.0304-0.05880.2679-0.19370.0080.48650.0761-0.04820.6361-0.0150.47361.255734.5319-20.7073
51.4630.81460.01841.4468-0.35620.60210.0571-0.1152-0.01920.0724-0.0490.02390.0866-0.0363-0.00010.42970.06060.00510.39080.00450.29535.655318.519244.4868
60.20680.37550.01940.8775-0.36350.8267-0.1213-0.25180.09710.74460.16020.0698-0.3999-0.1111-0.00850.402-0.00180.0370.4309-0.07760.32519.888433.6477-51.9111
71.29430.22621.10690.88420.96861.58420.07610.1578-0.2822-0.34850.1456-0.16140.29030.7097-0.00060.51950.00990.0360.866-0.03670.594928.501921.6673-63.8454
81.1052-0.42740.05811.48760.7832.09340.10580.35460.4885-0.5464-0.2856-0.0015-0.764-0.07040.00051.03830.00670.01440.67350.30670.963117.701890.3179-23.6814
91.1067-0.26390.06091.60910.89940.87980.1071-0.1077-0.12370.5656-0.2589-0.67880.23810.44210.00330.42130.1331-0.0340.59890.01480.448231.236333.5438-12.9116
100.36970.1282-0.26140.2491-0.08770.18050.4078-0.3633-0.3646-0.0578-0.09440.2541-0.2084-0.1428-00.4822-0.04770.00260.75380.01140.577630.886943.2611-19.6264
110.3259-0.13320.41780.06330.03020.8012-0.02450.0121-0.19120.21840.1614-0.0736-0.21150.0627-0.00070.58620.08540.05160.6427-0.05850.504224.143525.4949-37.7604
121.63550.31330.1941.2612-0.03090.3316-0.11880.2750.0905-0.1264-0.1311-0.068-0.1469-0.0201-00.60440.03260.0310.5283-0.04040.45748.624314.4101-68.3215
131.46870.4883-0.56811.3026-0.03282.0872-0.10540.12620.22920.49270.1285-0.2109-0.48550.7497-0.0260.8187-0.291-0.27510.95510.11920.819846.036554.91940.0076
140.2262-0.22480.05960.2327-0.06730.0191-0.39030.0423-0.11660.19720.0816-0.5203-0.90.98990.00030.8907-0.2826-0.20041.26730.1641.028453.132753.840935.9432
150.33060.23280.14240.28490.15690.07730.20950.25820.4006-0.0496-0.0135-0.26310.18880.0555-0.00090.87910.2124-0.04360.81540.11441.2778-37.7272106.8686-0.8573
160.36770.0447-0.00680.2481-0.17340.11110.1214-0.04260.46340.0964-0.28590.2023-0.67420.24460.00021.44650.2452-0.00810.9143-0.12561.3321-24.568792.638729.9939
170.1661-0.1162-0.06860.5434-0.39050.4128-0.3617-0.08990.1668-0.2197-0.00310.60970.7902-0.20020.00070.51190.0564-0.00110.6032-0.09080.5472-12.465527.549649.5637
180.5413-0.1609-0.45920.42390.03530.79960.2340.0919-0.67220.12120.155-0.18950.2226-0.24880.00580.47990.03340.05310.65220.2470.5737-15.606928.532840.9944
191.3761-0.36650.4671.932-1.0311.72020.02540.1673-0.1847-0.0714-0.0164-0.30610.03360.23980.00030.59850.0983-0.01950.632-0.01120.49626.367819.107234.8778
200.0844-0.14650.1160.82680.28190.5920.1066-0.40980.070.3601-0.22921.38170.4808-0.4056-0.01930.9349-0.1564-0.13220.81860.18161.4798-29.77269.271818.655
210.6889-0.73690.29840.7265-0.34380.13180.2446-0.0705-0.114-0.2834-0.02780.29980.2323-0.3978-0.00011.0604-0.0081-0.05841.2721-0.15161.1056-33.47225.1395-13.0316
220.0267-0.0003-0.02150.0113-0.00110.01370.04190.89260.0693-0.1664-0.4040.0598-0.3672-0.29890.00122.9951-0.3067-0.02132.27540.07431.8719-11.931268.5281-12.2018
230.06730.0397-0.00010.0242-0.00010.02910.0417-0.0569-0.0097-0.32510.29550.5591-0.5408-0.72960.00061.59070.1432-0.312.9914-0.05392.0135-13.244543.50219.1441
240.2248-0.0916-0.05690.0530.09480.34350.1865-0.1842-0.46320.1176-0.51661.1259-0.0977-0.8903-0.00052.4186-0.0891-0.04261.9212-0.01241.9605-13.713751.8317-3.9556
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 2:825
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 826:1455
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 20:1103
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 1104:1224
5X-RAY DIFFRACTION5CHAIN C
6X-RAY DIFFRACTION6CHAIN D AND RESSEQ 4:66
7X-RAY DIFFRACTION7CHAIN D AND RESSEQ 67:221
8X-RAY DIFFRACTION8CHAIN E
9X-RAY DIFFRACTION9CHAIN F AND RESSEQ 72:130
10X-RAY DIFFRACTION10CHAIN F AND RESSEQ 131:155
11X-RAY DIFFRACTION11CHAIN G AND RESSEQ 1:80
12X-RAY DIFFRACTION12CHAIN G AND RESSEQ 81:171
13X-RAY DIFFRACTION13CHAIN H AND RESSEQ 2:128
14X-RAY DIFFRACTION14CHAIN H AND RESSEQ 129:146
15X-RAY DIFFRACTION15CHAIN I AND RESSEQ 2:52
16X-RAY DIFFRACTION16CHAIN I AND RESSEQ 53:120
17X-RAY DIFFRACTION17CHAIN J AND RESSEQ 1:40
18X-RAY DIFFRACTION18CHAIN J AND RESSEQ 41:65
19X-RAY DIFFRACTION19CHAIN K
20X-RAY DIFFRACTION20CHAIN L
21X-RAY DIFFRACTION21CHAIN M
22X-RAY DIFFRACTION22CHAIN N
23X-RAY DIFFRACTION23CHAIN P
24X-RAY DIFFRACTION24CHAIN T

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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