[日本語] English
万見
- PDB-3k1f: Crystal structure of RNA Polymerase II in complex with TFIIB -

+
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: 3k1f
タイトルCrystal structure of RNA Polymerase II in complex with TFIIB
要素
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Transcription initiation factor IIB
キーワードTRANSCRIPTION / RNA Polymerase II / TFIIB / Transcription Factor / Transcription Initiation / DNA-binding / DNA-directed RNA polymerase / Isopeptide bond / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Zinc-finger / DNA damage / DNA repair / mRNA processing / Initiation factor
機能・相同性
機能・相同性情報


transcription preinitiation complex assembly / 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 ...transcription preinitiation complex assembly / 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / RNA polymerase II complex binding / 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 / Dual incision in TC-NER / transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase II preinitiation complex assembly / : / translation initiation factor binding / TBP-class protein binding / translation initiation factor activity / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / mRNA processing / cytoplasmic stress granule / 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 / metal ion binding / nucleus / cytoplasm
類似検索 - 分子機能
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 / Zinc finger, TFIIB-type / TFIIB zinc-binding / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat ...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 / Zinc finger, TFIIB-type / TFIIB zinc-binding / 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 / 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 / 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. / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3
類似検索 - ドメイン・相同性
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 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: 4.3 Å
データ登録者Kostrewa, D. / Zeller, M.E. / Armache, K.-J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P.
引用ジャーナル: Nature / 年: 2009
タイトル: RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
著者: Kostrewa, D. / Zeller, M.E. / Armache, K.J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P.
履歴
登録2009年9月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02009年11月10日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22013年5月1日Group: Other
改定 1.32023年9月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: DNA-directed RNA polymerase 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 RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: Transcription initiation factor IIB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)533,43822
ポリマ－532,85013
非ポリマー5899
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 area74640 Å2
ΔGint-325 kcal/mol
Surface area155330 Å2
手法PISA
単位格子
Length a, b, c (Å)220.97, 408.27, 275.24
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 B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / 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 / DNA-directed RNA polymerase II 140 kDa polypeptide / B150


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 B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa ...RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa polypeptide / B44.5


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, DNA-directed RNA polymerase
#4: タンパク質 DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II 32 kDa polypeptide / B32


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, DNA-directed RNA polymerase
#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, DNA-directed RNA polymerase
#9: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6


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, DNA-directed RNA polymerase
#11: タンパク質 DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.6 kDa polypeptide / B13.6


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 polymerase

-
DNA-directed RNA polymerases I, II, and III subunit ... , 5種, 5分子 EFHJL

#5: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 kDa polypeptide / ABC27


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, DNA-directed RNA polymerase
#6: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 kDa polypeptide / ABC23


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, DNA-directed RNA polymerase
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 kDa polypeptide / ABC14.5 / ABC14.4


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, DNA-directed RNA polymerase
#10: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 kDa polypeptide / ABC10-beta / ABC8


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, DNA-directed RNA polymerase
#12: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


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-directed RNA polymerase

-
タンパク質 / 非ポリマー , 2種, 10分子 M

#13: タンパク質 Transcription initiation factor IIB


分子量: 18691.453 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: B3LK56, UniProt: P29055*PLUS
#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

-
詳細

配列の詳細THE B-LINKER AND B-CYCLIN DOMAIN OF TFIIB (CHAIN M, RESIDUES 84-214) WERE FITTED AS POLY-ALANINE ...THE B-LINKER AND B-CYCLIN DOMAIN OF TFIIB (CHAIN M, RESIDUES 84-214) WERE FITTED AS POLY-ALANINE USING UNK RESIDUE NAMES DUE TO EXPERIMENTAL UNCERTAINTY IN THE ELECTRON DENSITY MAPS ABOUT THE EXACT SEQUENCE ASSIGNMENT RELATIVE TO THE S. CEREVISIAE AMINO ACID SEQUENCE. RESIDUES 215-345 WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THE COMPLETE CRYSTALLIZED SEQUENCE FOR THE CHAIN M IS AS FOLLOWS: MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRS EWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKK DNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRA EVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCS HLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVT EGTIKSGYKILYEHRDKLVDPQLIANGVVSLDSLPGVEKK

-
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: 5.82 Å3/Da / 溶媒含有率: 78.88 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 800 mM sodium ammonium tartrate, 100 mM HEPES pH 7.5, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
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: ESRF / ビームライン: ID29 / 波長: 0.934 Å
検出器タイプ: ADSC QUANTUM 4 / 検出器: CCD / 詳細: silicon crystal monochromator
放射モノクロメーター: Silicon crystal monochromator / 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: 0.934 Å / 相対比: 1
反射解像度: 4.3→40 Å / Num. all: 83919 / Num. obs: 83919 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / 冗長度: 4.7 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.13 / Net I/σ(I): 11.5
反射 シェル解像度: 4.3→4.3 Å / 冗長度: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 6050 / Rsym value: 0.99 / % possible all: 98.2

-
解析

ソフトウェア
名称バージョン分類
ADSCQuantumデータ収集
PHASER位相決定
BUSTER2.7.0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: First 12-subunit RNA Polymerase II from PDB entry 3HOU

3hou


解像度: 4.3→39.69 Å
Isotropic thermal model: Overall anisotropic temperature factor, one TLS group for all atoms, one group isotropic temperature factor for each residue
交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
詳細: REFINEMENT WAS DONE AGAINST THE STRUCTURE FACTORS WITH FRIEDEL PAIRS MERGED AND A SHARPENING B-FACTOR OF -80 A**2 APPLIED. THE STRUCTURE WAS REFINED WITH ONE TLS GROUP FOR ALL ATOMS AND ...詳細: REFINEMENT WAS DONE AGAINST THE STRUCTURE FACTORS WITH FRIEDEL PAIRS MERGED AND A SHARPENING B-FACTOR OF -80 A**2 APPLIED. THE STRUCTURE WAS REFINED WITH ONE TLS GROUP FOR ALL ATOMS AND ISOTROPIC GROUP B-FACTORS FOR WHOLE RESIDUES. ADDITIONAL DISTANCE RESTRAINTS WERE APPLIED TO STABILIZE THE ZINC COORDINATION SPHERE AND SECONDARY STRUCTURAL ELEMENTS. THE BUSTER ELECTRON DENSITY MAP COEFFICIENTS ARE AVAILABLE UPON REQUEST FROM DIRK KOSTREWA.
Rfactor反射数%反射Selection details
Rfree0.255 2058 2.45 %RANDOM
Rwork0.22 ---
all0.221 83918 --
obs0.221 83918 99.4 %-
原子変位パラメータBiso mean: 124.4 Å2
Baniso -1Baniso -2Baniso -3
1-16.7149 Å20 Å20 Å2
2--25.3097 Å20 Å2
3----42.0246 Å2
Refine analyzeLuzzati coordinate error obs: 1.13 Å
精密化ステップサイクル: LAST / 解像度: 4.3→39.69 Å
タンパク質核酸リガンド溶媒全体
原子数32323 0 9 0 32332
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_angle_deg1.16
LS精密化 シェル解像度: 4.3→4.41 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.27 136 2.25 %
Rwork0.251 5908 -
obs-5908 99.4 %
精密化 TLS手法: refined / Origin x: 97.8862 Å / Origin y: 54.753 Å / Origin z: -2.3668 Å
111213212223313233
T0.1762 Å2-0.0337 Å20.1422 Å2--0.2862 Å20.0175 Å2--0.04 Å2
L0.7876 °2-0.0127 °2-0.0916 °2-0.8986 °2-0.0346 °2--0.7701 °2
S0.061 Å °0.0042 Å °0.2847 Å °0.3383 Å °-0.1643 Å °0.1776 Å °-0.0591 Å °-0.0789 Å °0.1033 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }A2 - 1455
2X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }A3006 - 3008
3X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }C3 - 268
4X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }C3002
5X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }B20 - 1224
6X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }B3007
7X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }E2 - 215
8X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }D3 - 221
9X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }G1 - 171
10X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }F69 - 155
11X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }I2 - 120
12X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }I3003 - 3004
13X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }H2 - 146
14X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }K1 - 114
15X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }J1 - 65
16X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }J3001
17X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }M13 - 214
18X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }M3009
19X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }L25 - 70
20X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }L3005

+
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