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- PDB-4bbr: Structure of RNA polymerase II-TFIIB complex -

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基本情報

登録情報
データベース: PDB / ID: 4bbr
タイトルStructure of 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
  • TRANSCRIPTION INITIATION FACTOR IIB
キーワードTRANSCRIPTION / RNA POLYMERASE / TFIIB
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 / RNA polymerase II core complex assembly / positive regulation of transcription regulatory region DNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA ...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 / RNA polymerase II core complex assembly / positive regulation of transcription regulatory region DNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / 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 II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / acetyltransferase activity / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / 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 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / 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. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 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, 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / 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, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4
類似検索 - ドメイン・相同性
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 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 / OTHER / 解像度: 3.4 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 1.12012年11月28日Group: Database references
改定 1.22013年1月30日Group: Database references
改定 1.32019年11月20日Group: Derived calculations / Other
カテゴリ: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
改定 1.42024年5月8日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 6-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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)553,05324
ポリマ－552,41613
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 area82680 Å2
ΔGint-448 kcal/mol
Surface area194510 Å2
手法PISA
単位格子
Length a, b, c (Å)222.440, 386.760, 254.350
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 / RPB1 / RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RPB1 / 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 / RPB2 / RNA POLYMERASE II SUBUNIT 2 / B150 / 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 / RPB3 / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA ...RPB3 / 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 / 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 / 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 / RPB9 / RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / ...RPB9 / 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 / 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

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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 / RPB5 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / ...RPB5 / 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 / RPB6 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / ...RPB6 / 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 / RPB8 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA ...RPB8 / 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 / RPB10 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA ...RPB10 / 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 / RPB12 / 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

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タンパク質 , 1種, 1分子 M

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


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

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非ポリマー , 2種, 11分子

#14: 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
#15: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg

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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: 4.95 Å3/Da / 溶媒含有率: 75.16 % / 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: 3.4→50 Å / Num. obs: 149750 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / 冗長度: 7.7 % / Biso Wilson estimate: 67.78 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 7.8

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解析

ソフトウェア名称: BUSTER / バージョン: 2.11.2 / 分類: 精密化
精密化構造決定の手法: OTHER
開始モデル: NONE

解像度: 3.4→49.41 Å / Cor.coef. Fo:Fc: 0.9111 / Cor.coef. Fo:Fc free: 0.8737 / SU R Cruickshank DPI: 0.787 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.67 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.335
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=32789. 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=32789. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=11.
Rfactor反射数%反射Selection details
Rfree0.211 2995 2 %RANDOM
Rwork0.1745 ---
obs0.1753 149749 99.96 %-
原子変位パラメータBiso mean: 75.56 Å2
Baniso -1Baniso -2Baniso -3
1--15.7464 Å20 Å20 Å2
2--13.2984 Å20 Å2
3---2.4479 Å2
Refine analyzeLuzzati coordinate error obs: 0.582 Å
精密化ステップサイクル: LAST / 解像度: 3.4→49.41 Å
タンパク質核酸リガンド溶媒全体
原子数32789 0 11 0 32800
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0133370HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3345058HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12016SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes899HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4776HARMONIC5
X-RAY DIFFRACTIONt_it33370HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion24.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4415SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance38HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39268SEMIHARMONIC4
LS精密化 シェル解像度: 3.4→3.49 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2904 220 2 %
Rwork0.2341 10778 -
all0.2353 10998 -
obs--99.96 %
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)
16.2858-0.84950.45422.5018-0.15712.82760.05850.1981-0.65450.2529-0.03770.21780.2233-0.2381-0.02080.03250.0548-0.0260.3769-0.0958-0.3942-10.920128.7193-29.9229
22.39350.1807-0.20612.5596-0.19221.69810.02250.40440.5598-0.3014-0.15290.2071-0.3636-0.1450.1304-0.01060.1513-0.08860.36190.0597-0.207-17.990756.2553-34.8445
30.86040.06690.6260.3799-0.17171.61380.03640.0533-0.01850.0173-0.0474-0.10680.10790.24980.0111-0.2321-0.00810.03330.10480.0213-0.325718.98636.453910.9346
40.9183-1.34320.35012.338-0.19570.2295-0.033-0.10280.51620.1667-0.132-0.2131-0.43310.02810.16510.075-0.05080.07010.1145-0.0328-0.172-2.751670.576129.6218
52.03960.61640.17631.0082-0.23690.73040.0609-0.04870.21430.005-0.105-0.1816-0.25660.15660.0441-0.1179-0.07910.01210.10430.1151-0.137433.527165.7074-0.3876
66.5605-3.1459-0.14881.7390.33230.3247-0.1168-0.20790.8002-0.01570.0422-0.1186-0.147-0.20080.07460.03220.0822-0.02980.14260.05120.5142-5.4071103.7722.2905
70.3660.02640.3820.6450.25960.6484-0.0030.15680.3008-0.0736-0.1173-0.0287-0.16470.0120.1202-0.13730.01920.0220.1990.1226-0.199810.636857.2318-13.8443
81.3104-0.22110.18671.19570.07510.44280.0165-0.07390.0029-0.24290.010.5594-0.1358-0.4116-0.0266-0.1230.107-0.10380.45630.02720.0137-44.368744.765513.7066
94.43520.36681.19784.921-0.41373.61860.04210.2131-0.1988-0.46930.09220.10860.35650.0286-0.13430.23860.2609-0.15650.27540.03170.202-40.290981.6697-1.2126
101.73260.56091.00651.06110.59311.6939-0.02320.28190.1712-0.4510.02060.2385-0.0775-0.11760.00260.0010.1087-0.04950.3950.0423-0.1037-33.74249.58967.5961
111.3012-0.6391.13932.2872-1.09322.5081-0.1021-0.35580.41480.42590.08680.3908-0.3639-0.39780.0153-0.00540.20410.07180.4515-0.03420.0367-37.105769.154731.6904
120-0.2839-0.14670.1873-0.51581.1389-0.0519-0.1840.0927-0.00860.06290.0989-0.1746-0.2278-0.011-0.19090.0002-0.03680.1028-0.0767-0.2773-13.003743.244330.3356
132.90890.16522.59111.35330.65684.65960.09980.3588-0.3075-0.46830.03340.20920.22290.0183-0.13320.0433-0.0744-0.06270.156-0.0047-0.2694-18.799816.07598.6999
140.6389-0.04050.07130.2253-0.08911.05650.05910.03750.05220.02430.024-0.00560.1101-0.0766-0.0831-0.19860.0533-0.02760.0149-0.0192-0.32311.376337.98678.6799
150.89210.1870.17390.6264-0.18930.5402-0.0334-0.1303-0.0688-0.065-0.00680.04550.0855-0.030.0402-0.0709-0.02170.00230.22350.0341-0.34455.727918.643644.4981
161.5657-0.00751.06642.3756-0.73994.4492-0.10180.0898-0.0670.08650.1243-0.0945-0.09060.3378-0.0225-0.1051-0.02850.04190.349-0.0181-0.279625.439126.1538-59.573
171.2716-0.43530.0373.49220.31011.98850.1270.34190.6852-0.7489-0.03670.0769-0.77470.0525-0.09030.3683-0.0614-0.00110.35090.31880.301318.051790.5112-23.3626
182.2239-1.1008-0.0555.1265-0.18813.39610.16830.06810.0218-0.0463-0.0823-0.19450.2780.278-0.086-0.27530.0314-0.05270.29660.0214-0.356831.267136.5821-15.0982
190.54270.4890.82580.43521.38542.54580.00250.0615-0.15620.00240.1098-0.00130.21710.1736-0.1123-0.07950.04440.02940.1908-0.0112-0.287616.200519.8922-53.5123
204.62362.80610.08485.0746-0.45992.9148-0.0406-0.14450.12790.19880.1238-0.7894-0.22770.573-0.08320.0555-0.2519-0.25330.47640.0978-0.057347.168154.852939.4466
211.696-0.7428-0.04181.961-0.76150.3175-0.07290.25240.45460.4-0.12770.0553-0.08450.10980.20060.26920.20920.00290.1871-0.10430.3262-30.180199.125816.4808
220-0.8014-0.68561.0531-1.19414.4924-0.0141-0.26810.05970.327-0.01030.08390.0291-0.07190.0244-0.25140.04040.05170.198-0.0212-0.3269-13.858427.943945.8947
232.80240.51060.19641.155-1.31342.9476-0.0413-0.0349-0.0890.2264-0.0406-0.3078-0.03040.29840.082-0.1550.1084-0.0310.081-0.0312-0.323726.662719.114635.1116
244.7742.57723.17580.14561.33273.37920.01650.0254-0.24920.20660.00020.57460.1968-0.2384-0.01660.1769-0.1901-0.07320.28270.17970.1317-29.28129.200118.2894
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3-81
2X-RAY DIFFRACTION2CHAIN A AND RESID 82-323
3X-RAY DIFFRACTION3CHAIN A AND RESID 324-659
4X-RAY DIFFRACTION4CHAIN A AND RESID 660-831
5X-RAY DIFFRACTION5CHAIN A AND RESID 832-1127
6X-RAY DIFFRACTION6CHAIN A AND RESID 1128-1329
7X-RAY DIFFRACTION7CHAIN A AND RESID 1330-1454
8X-RAY DIFFRACTION8CHAIN B AND RESID 20-234
9X-RAY DIFFRACTION9CHAIN B AND RESID 235-392
10X-RAY DIFFRACTION10CHAIN B AND RESID 393-539
11X-RAY DIFFRACTION11CHAIN B AND RESID 540-735
12X-RAY DIFFRACTION12CHAIN B AND RESID 736-841
13X-RAY DIFFRACTION13CHAIN B AND RESID 842-974
14X-RAY DIFFRACTION14CHAIN B AND RESID 975-1224
15X-RAY DIFFRACTION15CHAIN C AND RESID 3-268
16X-RAY DIFFRACTION16CHAIN D AND RESID 4-221
17X-RAY DIFFRACTION17CHAIN E AND RESID 2-215
18X-RAY DIFFRACTION18CHAIN F AND RESID 72-155
19X-RAY DIFFRACTION19CHAIN G AND RESID 1-171
20X-RAY DIFFRACTION20CHAIN H AND RESID 2-146
21X-RAY DIFFRACTION21CHAIN I AND RESID 2-120
22X-RAY DIFFRACTION22CHAIN J AND RESID 1-65
23X-RAY DIFFRACTION23CHAIN K AND RESID 2-114
24X-RAY DIFFRACTION24CHAIN L AND RESID 27-70

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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://pdbjlvh1.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