[日本語] English
万見
- PDB-4by1: elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP -

+
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: 4by1
タイトルelongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP
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*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3'
  • 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP *TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*AP*T)-3'
  • 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'
  • TRANSCRIPTION FACTOR BYE1
キーワードTRANSCRIPTION
機能・相同性
機能・相同性情報


RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / termination of RNA polymerase II transcription ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / 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 Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / 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 / 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 / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / 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 by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / DNA-templated transcription initiation / P-body / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / 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 / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / 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
Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / RNA Polymerase II, Rpb4 subunit / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 ...Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / RNA Polymerase II, Rpb4 subunit / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / 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 / 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 Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / 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 / RNA polymerase Rpb4/RPC9, core / Eukaryotic RNA polymerase II heptapeptide repeat. / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / 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 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / 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
類似検索 - ドメイン・相同性
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA / DNA (> 10) / RNA / RNA (> 10) / 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 ...DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA / DNA (> 10) / RNA / RNA (> 10) / 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 / DNA-directed RNA polymerase II subunit RPB7 / Transcription factor BYE1 / 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)
SYNTHETIC CONSTRUCT (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.6 Å
データ登録者Kinkelin, K. / Wozniak, G.G. / Rothbart, S.B. / Lidschreiber, M. / Strahl, B.D. / Cramer, P.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2013
タイトル: Structures of RNA Polymerase II Complexes with Bye1, a Chromatin-Binding Phf3/Dido1 Homologue
著者: Kinkelin, K. / Wozniak, G.G. / Rothbart, S.B. / Lidschreiber, M. / Strahl, B.D. / Cramer, P.
履歴
登録2013年7月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02013年9月11日Provider: repository / タイプ: Initial release
改定 1.12013年10月2日Group: Database references
改定 1.22019年1月30日Group: Data collection / Experimental preparation / Other
カテゴリ: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
改定 1.32019年2月6日Group: Data collection / Experimental preparation / カテゴリ: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
改定 1.42023年12月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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 "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BN" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" 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 "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
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 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
N: 5'-D(*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3'
P: 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'
T: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP *TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*AP*T)-3'
X: TRANSCRIPTION FACTOR BYE1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)548,11426
ポリマ－547,06116
非ポリマー1,05310
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 area84390 Å2
ΔGint-423.3 kcal/mol
Surface area199840 Å2
手法PQS
単位格子
Length a, b, c (Å)222.240, 391.580, 281.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
要素

-
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


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 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


分子量: 138951.328 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


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 / 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


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 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA- ...RNA POLYMERASE II SUBUNIT B9 / B12.6 / 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 / 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

-
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 / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / 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 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / 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 / 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 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 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / 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


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

-
DNA鎖 , 2種, 2分子 NT

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


分子量: 4303.828 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物)
#15: DNA鎖 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP *TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*AP*T)-3' / DNA TEMPLATE STRAND


分子量: 7983.981 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物)

-
RNA鎖 / タンパク質 , 2種, 2分子 PX

#14: RNA鎖 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' / RNA PRODUCT STRAND


分子量: 3506.154 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物)
#16: タンパク質 TRANSCRIPTION FACTOR BYE1 / BYPASS OF ESS1 PROTEIN 1


分子量: 17094.592 Da / 分子数: 1 / Fragment: RESIDUES 225-370 / 由来タイプ: 組換発現
由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母)
プラスミド: POPINF / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): RIL / 参照: UniProt: P36106

-
非ポリマー , 3種, 10分子

#17: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 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: 1 / 由来タイプ: 合成 / 式: Mg
#19: 化合物 ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE / α,β-メチレンATP


分子量: 505.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C11H18N5O12P3
コメント: AMP-CPP, エネルギー貯蔵分子類似体*YM

-
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: 5.2 Å3/Da / 溶媒含有率: 76 % / 解説: NONE
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 5-7% PEG6000, 50 MM HEPES PH 7.0, 200 MM AMMONIUM ACETATE, 300 MM SODIUM ACETATE, 5 MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293 K

-
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: 0.91887
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年4月1日
放射モノクロメーター: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR 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: 0.91887 Å / 相対比: 1
反射解像度: 3.6→48.95 Å / Num. obs: 141065 / % possible obs: 100 % / Observed criterion σ(I): 0 / 冗長度: 7.62 % / Biso Wilson estimate: 79.08 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 9.95
反射 シェル解像度: 3.6→3.69 Å / 冗長度: 7.61 % / Mean I/σ(I) obs: 1.57 / % possible all: 100

-
解析

ソフトウェア
名称バージョン分類
BUSTER2.11.5精密化
XDSデータ削減
XSCALEデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 1WCM

1wcm


解像度: 3.6→48.95 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 1.205 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.936 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.358
詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=33017. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...詳細: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=33017. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=9.
Rfactor反射数%反射Selection details
Rfree0.2062 2784 1.97 %RANDOM
Rwork0.1749 ---
obs0.1755 141062 99.98 %-
原子変位パラメータBiso mean: 125.34 Å2
Baniso -1Baniso -2Baniso -3
1--11.2902 Å20 Å20 Å2
2--4.7097 Å20 Å2
3---6.5805 Å2
Refine analyzeLuzzati coordinate error obs: 0.854 Å
精密化ステップサイクル: LAST / 解像度: 3.6→48.95 Å
タンパク質核酸リガンド溶媒全体
原子数32061 925 40 0 33026
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0133695HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2945687HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12010SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes891HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4688HARMONIC5
X-RAY DIFFRACTIONt_it33695HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion24.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4454SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance82HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39557SEMIHARMONIC4
LS精密化 シェル解像度: 3.6→3.69 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2645 204 1.97 %
Rwork0.2371 10172 -
all0.2377 10376 -
obs--99.98 %
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)
16.4830.58842.30553.90980.50572.7470.05840.5282-0.4480.1142-0.08150.18170.4252-0.38610.0232-0.3514-0.00990.2133-0.0079-0.012-0.043497.997232.087-37.7831
23.030.6332-0.08533.3769-0.16823.15-0.03040.37710.5895-0.25-0.11860.3799-0.4338-0.49770.149-0.40450.183-0.01070.01730.22150.057491.344760.0608-41.2196
30.95730.10620.22170.7868-0.32111.590.0156-0.09490.23570.3389-0.11-0.22760.08670.29310.0944-0.2043-0.02090.0216-0.21510.07180.1832124.31836.56865.9085
42.6759-1.3807-0.47742.32350.3410.86570.0374-0.16040.99270.6717-0.16820.1074-0.49090.08660.13080.1193-0.08790.1889-0.412-0.19930.5402101.71168.939926.042
52.84330.75310.36511.2018-0.00280.7190.1424-0.22650.16760.2309-0.0969-0.36-0.14710.1299-0.0455-0.3566-0.11470.0256-0.32980.10270.4714139.55366.7511-1.8084
68.2461-4.05180.28983.4493-0.22640.4968-0.1334-0.23450.82280.0024-0.0007-0.021-0.3904-0.2650.1341-0.40030.10890.0247-0.5349-0.1550.607999.9867106.149-1.4006
70.7628-0.50150.55512.15330.07461.0393-0.0210.11470.5666-0.0488-0.0680.1309-0.18180.1070.0889-0.41180.00870.1523-0.17770.18060.4024118.16859.4883-17.9799
80.9501-0.3405-0.1742.8192-0.34610.82470.1315-0.18860.17980.07460.10420.8680.0899-0.6305-0.2357-0.43010.01570.2372-0.04910.05710.492365.293143.936610.1244
97.0563-1.28672.64478.2204-0.31726.07250.05380.3747-0.5179-0.19520.16970.0590.1842-0.0982-0.2234-0.40280.2380.2021-0.4673-0.10.551865.657483.2173-5.4911
102.62370.84430.86642.03520.74522.4619-0.03060.29890.5733-0.14760.03890.4963-0.1161-0.4221-0.0083-0.28620.16150.2341-0.18770.12910.279473.540551.16941.526
111.2293-2.080.10181.5275-1.13193.3588-0.0699-0.57720.7040.49960.00460.1741-0.3504-0.60910.0653-0.31960.17750.304-0.3131-0.10930.453867.43567.868426.0447
120.00510.2885-0.31420.3231-0.87060.8714-0.0242-0.17530.16520.40270.12390.3028-0.0785-0.3671-0.0997-0.0081-0.02740.2068-0.1882-0.14930.190191.261441.91123.7575
133.23891.26552.52934.10662.17616.92050.12520.53670.0039-0.87580.09020.39680.2741-0.1264-0.21540.0481-0.20410.1132-0.31740.0927-0.05385.868216.5508-0.5944
141.03250.0846-0.17750.7306-0.10091.79360.0685-0.09730.2460.30950.00930.03950.2549-0.0763-0.0778-0.1682-0.00060.061-0.3443-0.0140.1402107.20138.31722.5641
151.72690.1980.05171.35790.07880.7980.0138-0.5615-0.16430.5931-0.04970.04980.2227-0.02540.0360.2585-0.01570.1233-0.21440.1103-0.1999108.79515.86336.6916
161.4809-0.41911.8261.703-1.04786.2169-0.08810.1197-0.25610.27820.0283-0.04440.32540.84870.0598-0.36480.19340.0940.2034-0.0450.0645137.01329.5617-65.0641
171.81850.36950.12855.4745-0.1171.7469-0.00420.29930.7191-0.7834-0.1123-0.1346-0.79990.03690.1166-0.1507-0.04490.0553-0.440.3040.5698126.38892.843-25.2185
182.66730.30460.2017.6327-1.10613.98170.0074-0.08090.187-0.0923-0.0349-0.28970.43190.14060.0275-0.34430.08310.0299-0.04170.06460.206138.7638.7059-18.6392
1900.26880.87111.51832.15535.51470.04860.1199-0.34580.11430.12670.03560.73190.3322-0.1753-0.23680.1680.13450.06930.01520.1402126.53623.6141-58.9501
205.32121.63050.58333.6677-0.21033.5266-0.0534-0.7510.24070.5580.0614-0.5904-0.20690.8884-0.008-0.1744-0.2856-0.304-0.0029-0.0744-0.047150.53951.960237.7097
211.7838-1.2890.9322.1847-1.99070.0454-0.01770.40010.52510.4569-0.225-0.0146-0.01430.05870.2426-0.13030.25260.2086-0.5705-0.23590.607975.070798.952313.4332
223.5932-1.3914-2.0440.1371-1.47661.34910.096-0.34160.0920.5572-0.11510.18760.2363-0.09990.0190.2571-0.03860.2867-0.21530.0520.03789.263525.317437.7875
233.83950.52830.1842.565-0.51630.66940.0188-0.3522-0.2610.6226-0.1449-0.44550.38310.67450.12610.06840.1095-0.0355-0.17120.1292-0.07130.33316.943328.7512
243.26645.06092.2190.44540.974700.0342-0.0992-0.0267-0.0436-0.16650.60830.0838-0.24620.13230.0657-0.2680.1744-0.10470.02240.209475.13939.09228.6843
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|3 - A|81 }
2X-RAY DIFFRACTION2{ A|82 - A|323 }
3X-RAY DIFFRACTION3{ A|324 - A|659 }
4X-RAY DIFFRACTION4{ A|660 - A|831 }
5X-RAY DIFFRACTION5{ A|832 - A|1127 }
6X-RAY DIFFRACTION6{ A|1128 - A|1329 }
7X-RAY DIFFRACTION7{ A|1330 - A|1454 }
8X-RAY DIFFRACTION8{ B|20 - B|234 }
9X-RAY DIFFRACTION9{ B|235 - B|392 }
10X-RAY DIFFRACTION10{ B|393 - B|539 }
11X-RAY DIFFRACTION11{ B|540 - B|735 }
12X-RAY DIFFRACTION12{ B|736 - B|841 }
13X-RAY DIFFRACTION13{ B|842 - B|974 }
14X-RAY DIFFRACTION14{ B|975 - B|1224 }
15X-RAY DIFFRACTION15{ C|3 - C|268 }
16X-RAY DIFFRACTION16{ D|4 - D|221 }
17X-RAY DIFFRACTION17{ E|2 - E|215 }
18X-RAY DIFFRACTION18{ F|72 - F|155 }
19X-RAY DIFFRACTION19{ G|1 - G|171 }
20X-RAY DIFFRACTION20{ H|2 - H|146 }
21X-RAY DIFFRACTION21{ I|2 - I|120 }
22X-RAY DIFFRACTION22{ J|1 - J|65 }
23X-RAY DIFFRACTION23{ K|2 - K|114 }
24X-RAY DIFFRACTION24{ L|25 - L|70 }

+
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