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- PDB-5ot2: RNA polymerase II elongation complex in the presence of 3d-Napht-A -

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基本情報

登録情報
データベース: PDB / ID: 5ot2
タイトルRNA polymerase II elongation complex in the presence of 3d-Napht-A
要素
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA non-template strand
  • DNA template strand
  • RNA product strand
キーワードTRANSCRIPTION / Inhibitor / Complex / Polymerase
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 / transcription by RNA polymerase III / positive regulation of translational initiation / 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 / P-body / DNA-templated transcription initiation / 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 / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
類似検索 - 分子機能
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / 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 / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / 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 / N-terminal domain of TfIIb - #10 / 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 / 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 / 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 / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / S1 domain / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6
類似検索 - ドメイン・相同性
2-ethyl-7-methoxy-naphthalene / 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 ...2-ethyl-7-methoxy-naphthalene / 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 / 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: 3.2 Å
データ登録者Malvezzi, S. / Farnung, L. / Aloisi, C. / Angelov, T. / Cramer, P. / Sturla, S.J.
引用ジャーナル: Proc. Natl. Acad. Sci. U.S.A. / 年: 2017
タイトル: Mechanism of RNA polymerase II stalling by DNA alkylation.
著者: Malvezzi, S. / Farnung, L. / Aloisi, C.M.N. / Angelov, T. / Cramer, P. / Sturla, S.J.
履歴
登録2017年8月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年11月1日Provider: repository / タイプ: Initial release
改定 1.12017年11月15日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22017年11月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32019年2月20日Group: Advisory / Data collection / Derived calculations
カテゴリ: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
改定 1.42019年7月10日Group: Data collection / カテゴリ: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
改定 1.52024年11月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
改定 2.02025年7月30日Group: Atomic model / Data collection
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.value_order

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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

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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 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
T: DNA template strand
N: DNA non-template strand
P: RNA product strand
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)530,69625
ポリマ－529,96215
非ポリマー73410
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
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area71290 Å2
ΔGint-357 kcal/mol
Surface area155590 Å2
手法PISA
単位格子
Length a, b, c (Å)221.350, 394.930, 283.710
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 B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 138937.297 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38902

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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 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20434
#6: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20435
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20436
#10: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P22139
#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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P40422

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DNA鎖 , 2種, 2分子 TN

#13: DNA鎖 DNA template strand


分子量: 7841.912 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#14: DNA鎖 DNA non-template strand


分子量: 4359.852 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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RNA鎖 , 1種, 1分子 P

#15: RNA鎖 RNA product strand


分子量: 3602.202 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 3種, 10分子

#16: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 天然 / 式: Zn / 参照: DNA-directed RNA polymerase
#17: 化合物 ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 天然 / 式: Mg / 参照: DNA-directed RNA polymerase
#18: 化合物 ChemComp-AHW / 2-ethyl-7-methoxy-naphthalene


分子量: 186.250 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C13H14O

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 5.85 Å3/Da / 溶媒含有率: 78.96 %
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: 4-7% PEG 6000, 200 mM ammonium acetate, 300 mM sodium acetate, 50 mM HEPES pH 7.0, 5 mM TCEP

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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: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 0.976 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年7月24日
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: 0.976 Å / 相対比: 1
反射解像度: 3.2→49.882 Å / Num. obs: 202994 / % possible obs: 100 % / 冗長度: 13.5 % / Net I/σ(I): 16.38
反射 シェル解像度: 3.2→3.31 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.2→49.882 Å / SU ML: 0.42 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.22
Rfactor反射数%反射
Rfree0.2218 3272 0.83 %
Rwork0.1785 --
obs0.1789 202994 99.93 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.2→49.882 Å
タンパク質核酸リガンド溶媒全体
原子数30950 761 3 0 31714
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00732432
X-RAY DIFFRACTIONf_angle_d1.03343837
X-RAY DIFFRACTIONf_dihedral_angle_d6.2419680
X-RAY DIFFRACTIONf_chiral_restr0.0584934
X-RAY DIFFRACTIONf_plane_restr0.0075552
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.24770.32881440.321417083X-RAY DIFFRACTION100
3.2477-3.29850.31391260.317917143X-RAY DIFFRACTION100
3.2985-3.35260.3991450.330617006X-RAY DIFFRACTION100
3.3526-3.41040.38141480.313717020X-RAY DIFFRACTION100
3.4104-3.47240.33161450.287417116X-RAY DIFFRACTION100
3.4724-3.53910.28171450.257117113X-RAY DIFFRACTION100
3.5391-3.61130.26571380.242616987X-RAY DIFFRACTION100
3.6113-3.68980.2491400.22917091X-RAY DIFFRACTION100
3.6898-3.77560.28031500.224117115X-RAY DIFFRACTION100
3.7756-3.870.25341420.203117055X-RAY DIFFRACTION100
3.87-3.97460.23161490.188417023X-RAY DIFFRACTION100
3.9746-4.09150.24231450.172917100X-RAY DIFFRACTION100
4.0915-4.22350.23171360.163217044X-RAY DIFFRACTION100
4.2235-4.37440.22621380.151817116X-RAY DIFFRACTION100
4.3744-4.54940.17291440.141317070X-RAY DIFFRACTION100
4.5494-4.75630.20161500.135517061X-RAY DIFFRACTION100
4.7563-5.00690.22431380.141217110X-RAY DIFFRACTION100
5.0069-5.32020.17991420.149717063X-RAY DIFFRACTION100
5.3202-5.73050.20281410.166117083X-RAY DIFFRACTION100
5.7305-6.30610.21261450.178917135X-RAY DIFFRACTION100
6.3061-7.21630.25991500.182417047X-RAY DIFFRACTION100
7.2163-9.08280.18151270.157817117X-RAY DIFFRACTION100
9.0828-49.88780.18011440.167717022X-RAY DIFFRACTION100
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)
10.692-0.1235-0.04320.78960.00741.06390.0206-0.1453-0.3477-0.146-0.09960.04690.1451-0.057-00.93910.0026-0.07960.97820.11261.0293-2.6027-49.65218.3981
20.78090.2747-0.16180.35480.01350.1777-0.03830.146-0.6752-0.1197-0.0636-0.12750.1575-0.01180.00011.09450.0007-0.0891.13890.06951.61912.6974-77.74545.2702
30.61681.3824-0.24192.5702-0.00540.8490.08710.42010.03880.36590.01361.48650.3281-0.4906-0.00091.2615-0.0386-0.2371.3540.14532.2016-49.0166-43.2795-10.8663
40.82250.4830.15240.9131-0.27060.0723-0.0230.2368-0.1917-0.04410.16430.51590.0686-0.22070.00061.2867-0.0685-0.27361.35330.04831.7678-37.9832-50.5656-9.0584
51.33220.60590.392.0544-0.82512.4425-0.0182-0.14410.03920.49130.29920.1415-0.2460.03220.00091.2507-0.1678-0.0681.2435-0.1131.9143-45.7925-85.11717.1143
60.42250.5909-0.17041.3886-0.0529-0.0634-0.00540.0161-0.40190.22840.01420.54610.2244-0.05470.0021.3757-0.1045-0.19191.1910.06551.438-36.6745-57.0825-2.0636
70.9937-0.1326-0.48932.23870.05271.9601-0.18640.3605-0.3894-0.64460.10410.60070.1622-0.26180.00321.5617-0.2526-0.61191.4098-0.1091.7408-41.7122-68.4661-26.5609
81.1716-0.4283-0.24032.5785-0.28970.8477-0.1994-0.0556-0.1338-0.03160.15840.574-0.045-0.1584-0.00061.1090.0444-0.2211.05730.0120.8646-17.5607-30.8299-14.9891
90.6292-0.00760.09250.4166-0.08972.2767-0.0321-0.098-0.1272-0.2006-0.00870.0514-0.1031-0.11660.00020.9217-0.0229-0.06941.0540.06320.8671-1.6862-37.6519.2415
100.1185-0.0405-0.07460.2689-0.0740.07990.20190.2417-0.0181-0.4304-0.0220.1006-0.4004-0.07320.00071.75580.12060.0891.3950.08460.88889.4035-18.7876-50.0724
110.44370.40180.04060.36190.17150.2025-0.4958-0.2272-0.1289-0.11120.23790.32450.09110.5692-0.00011.42060.0031-0.07711.15340.22370.61282.1198-14.8509-31.487
121.30820.5718-0.67932.30920.061.27160.00890.34640.4067-0.49260.03110.3575-0.10390.00950.00021.49730.0574-0.31581.06120.11821.0404-15.7326-6.3614-29.5035
130.7363-0.32330.04040.12440.12720.1892-0.18230.4079-0.2095-0.36290.0782-0.17980.19150.2681-0.00051.7956-0.04820.01181.377-0.02680.90546.4507-34.5252-42.9461
140.9356-0.5138-0.00750.58580.32380.08110.04290.51280.035-0.6154-0.1017-0.405-0.14640.143-0.00081.72580.03910.02711.36080.21171.015914.6825-19.7937-40.4005
150.0562-0.00170.07160.04330.08970.1636-0.3259-1.1656-0.05160.1905-0.01930.67-0.2203-0.6968-0.00081.2282-0.1224-0.00851.940.03721.2358.1155-41.248253.3899
161.2393-0.449-0.34170.5265-0.7521.8766-0.19460.3003-0.0087-0.5830.18-0.2726-0.20860.87260.00021.2607-0.26480.00461.7226-0.10411.125828.2086-26.788558.5347
171.2365-0.4111-0.38760.99440.61771.185-0.2522-0.34660.2397-0.47020.2424-0.3161-0.17350.81820.00081.208-0.1077-0.08811.6764-0.10621.063624.9515-29.031272.1706
180.0612-0.0606-0.10680.14920.19550.2557-0.1452-0.5453-0.37140.31820.0536-0.5835-0.45420.75370.00121.2388-0.1469-0.0161.8284-0.21041.07131.3265-30.550882.8501
190.64960.06660.28510.15210.47941.13240.1869-0.0404-0.86850.6303-0.1628-0.35250.72240.16340.00241.71970.0341-0.10351.28730.34152.558517.0248-103.136623.356
200.0918-0.1259-0.14470.15520.21670.28-0.1492-0.92120.07910.84250.24850.5332-0.09710.1104-0.00261.8649-0.06830.19431.75510.62752.24477.6822-99.032337.2778
210.4069-0.02290.51421.75180.55820.79370.1963-0.4957-0.72890.3625-0.1294-0.20810.4693-0.13780.00041.1725-0.0166-0.14741.14750.38571.600517.0216-78.972224.029
220.05550.07140.06350.10260.08760.075-0.1712-0.97310.54480.7974-0.1342-0.7738-0.81050.1784-0.00391.1498-0.029-0.30061.35750.15451.304729.6176-51.247435.1544
230.07330.0459-0.02830.1028-0.0350.1402-0.2117-0.457-0.9482-0.2188-0.0582-0.16260.70961.20990.00281.01550.0215-0.07171.10980.14771.006930.9319-49.80419.2988
240.10680.0679-0.15630.0708-0.06720.22090.0360.2577-0.3769-0.55850.01550.728-0.2247-0.1889-0.00030.8660.0088-0.12331.01650.10840.724422.3936-35.593816.8728
250.0786-0.0420.0890.1483-0.06330.1090.4158-0.01610.32-0.14920.008-0.6359-0.55420.38240.00061.6044-0.0732-0.0251.26330.1741.114229.0032-23.303514.9977
260.07650.0253-0.00370.04330.00810.02160.17780.0062-0.1278-0.9564-0.0996-0.5790.1287-0.0980.00051.1158-0.11820.07451.29030.19170.929128.559-30.227511.6836
270.0444-0.008-0.02750.0163-0.01160.05960.29270.82760.0869-0.1232-0.1936-0.18030.56080.70740.00010.8495-0.0597-0.05941.04280.05841.248233.2589-33.606519.3102
280.0830.0383-0.01960.0244-0.02670.03080.047-0.2655-0.03531.03070.1213-0.4802-0.1333-0.6441-0.00080.9220.0281-0.08981.18690.2721.063323.2572-49.073528.1399
290.0137-0.0052-0.0080.03470.04830.05640.4364-0.1178-0.1031-0.3895-0.45590.1842-0.52270.0978-0.00211.0354-0.2302-0.04631.4373-0.02010.815329.2644-46.820227.2434
300.1217-0.0305-0.01260.0771-0.05910.0610.46371.3981-0.136-0.9289-0.30760.05360.25810.22080.00210.8964-0.0023-0.10561.30320.05461.255433.3019-43.146115.7115
31-0.02260.01780.00850.03050.05330.06490.2755-0.14450.3642-0.64370.4419-0.0960.3387-0.25460.0060.9659-0.1506-0.00821.5411-0.13440.91920.6683-31.651650.5348
320.00980.01460.03130.03620.07440.11950.0515-0.01740.5327-0.24390.4370.61-1.30380.19250.00091.4432-0.3364-0.06151.5732-0.02051.118225.272-23.639936.3624
330.02880.05990.1504-0.01410.14340.42490.0671-0.4690.1748-0.07540.1651-0.19110.0390.8029-0.00051.1567-0.2184-0.07041.59980.01031.107621.9891-30.588844.7807
340.76610.0715-0.11520.6562-0.09480.43160.0828-0.25840.35760.4213-0.22920.6746-0.4156-0.2301-0.0011.2687-0.0623-0.031.455-0.08221.15128.787-16.549275.4712
350.5312-0.5093-0.32430.47550.32630.19690.1632-0.25590.2658-0.17420.07670.1821-0.0970.5716-0.0031.2469-0.1072-0.01351.3902-0.00551.09739.173-23.357372.5702
360.1219-0.09430.19840.254-0.03290.2733-0.50470.5798-0.6789-0.51270.3165-0.45980.80870.22740.00111.89550.33880.49211.8002-0.17711.41237.7643-57.5833-40.1985
370.48510.15-0.14730.3048-0.2140.13140.42620.3940.0037-1.1379-0.4166-0.1407-0.4698-0.084-0.00111.60510.12610.47141.7101-0.01971.155439.5449-45.0777-38.8674
388.12791.64456.66264.45743.07486.1928-0.87540.82621.1047-0.2550.09220.4856-0.5079-0.0557-2.85741.1813-0.62370.67031.6250.66631.5343.7647-31.7088-39.7197
390.69540.32710.37610.23680.16490.2087-0.72840.720.86480.0056-0.25830.7133-0.1540.6138-0.0881.76110.32170.59271.87030.23331.700940.237-45.7935-37.2515
400.0482-0.0397-0.04680.1510.02530.05090.4368-0.0018-0.52850.29440.4638-0.5657-0.19240.12560.00021.78870.44780.20081.54410.03391.831144.9695-64.8504-25.9248
410.0862-0.08390.00760.0639-0.0060.029-0.120.408-1.3586-0.62380.1231-0.7718-0.05890.7489-0.00311.91680.42180.37611.40050.16431.702939.8132-57.9173-30.8331
420.03320.03510.01450.072-0.04770.1336-0.1289-0.4138-0.3044-0.0267-0.8153-0.1756-0.5910.1092-0.00492.15950.69050.21592.1903-0.0042.124349.8554-54.4178-28.9391
430.0357-0.00980.06120.0936-0.01480.0813-0.4240.50770.0854-0.2730.1089-0.5418-0.34290.1336-0.00381.76270.3210.45072.26070.39741.153442.8656-47.5925-41.8556
440.8549-0.516-0.49440.27020.2220.19550.1098-0.6428-0.0221-0.0603-0.1334-0.49270.12160.289-0.00021.2676-0.2811-0.06631.3732-0.02532.1692-42.138-109.39752.0376
450.7273-0.36590.12130.115-0.02460.0595-0.56660.3624-0.3006-0.8402-0.2560.96890.7088-0.1727-0.0012.2324-0.2855-0.41231.4304-0.23181.9928-29.3793-91.2974-27.2038
460.0781-0.07080.11540.0426-0.10470.1495-0.60620.31210.4977-0.8346-0.30880.3468-0.1662-0.4519-0.00571.49670.0973-0.30490.92060.15560.7881-13.8717-22.1831-34.3165
470.0584-0.0297-0.04970.0495-0.01250.0587-0.01320.9418-0.1083-0.03910.62910.43330.4386-0.43480.0021.6280.1632-0.5261.77250.00381.2176-25.8014-26.8797-45.4863
480.04030.05610.08440.19710.11120.1194-0.02210.7639-0.1295-0.46370.16920.50080.30140.03630.00051.66530.079-0.20361.28810.03070.8073-15.0442-29.551-40.6397
490.09510.0025-0.01280.05710.00370.0434-0.40750.01160.03050.2855-0.14660.1479-0.4312-0.7848-0.00171.4047-0.0132-0.32961.36940.15741.041-33.607-22.9394-25.7636
500.08410.0968-0.1110.111-0.13770.10230.0847-0.09740.6372-0.2192-0.0133-0.4776-0.76630.5884-0.00251.45170.0203-0.02341.230.15241.16266.8521-13.6116-15.3179
510.1133-0.1949-0.19420.31960.29850.3065-0.12750.8486-0.2859-0.0126-0.2741-0.53190.09110.4492-0.00141.26450.03410.10871.2060.08821.163926.2471-18.5752-18.9724
520.0588-0.04410.00970.0363-0.02450.055-0.14621.1575-0.8858-0.9009-0.031-0.23160.1060.0729-0.00281.40630.0640.22141.2650.18660.824925.3994-22.7018-30.9773
530.1034-0.11120.1070.1249-0.16550.1744-0.0679-0.52050.6932-0.3875-0.075-0.5074-0.34510.45220.00151.1323-0.08760.12121.30160.23671.167924.2132-21.6969-21.6672
540.1595-0.16750.00080.31710.18080.2768-0.06990.95480.5058-1.0590.0161-0.6637-0.33190.38840.01651.7262-0.15880.06161.570.35720.859319.8817-11.762-40.5628
550.09120.01730.04620.00110.00650.0194-0.37370.4152-0.1998-0.0532-0.6668-0.0142-0.1562-0.07540.0032.3036-0.01590.05852.03880.17870.83862.5543-10.9965-56.6862
560.02690.0023-0.0440.0465-0.06770.16150.1622-0.4085-0.05580.32780.41420.07570.4263-0.6462-0.00021.2966-0.05020.02621.19910.28921.3419-37.6071-8.1452-8.4759
570.2234-0.133-0.3760.07850.22220.6312-0.20860.27380.22790.01230.2389-0.196-0.11280.38450.34210.7424-0.0768-0.82430.90370.41582.1193-43.1461-13.9518-14.5826
580.0629-0.05210.02250.0534-0.01950.00470.1429-0.08230.61450.3581-0.87150.1773-0.6838-0.6199-0.01211.67480.26270.28181.53480.00651.9767-42.0875-7.1322-1.8859
591.4316-0.3659-0.6740.09330.17190.31810.49450.3350.1758-0.5266-0.18580.09270.0291-0.05880.30041.92030.8266-1.03521.1853-0.64972.9112-48.6787-11.5882-10.1593
600.06220.0557-0.010.05690.00280.08960.5204-0.1467-0.2259-0.7581-0.30291.1964-0.4918-0.30560.00591.32320.1681-0.28811.44980.24072.422-41.1479-15.9796-7.4337
610.03910.02070.02120.136-0.06680.07930.707-0.64620.7280.05880.36540.111-0.38240.37380.00311.62560.0556-0.1221.26060.10871.1795-18.7558-7.6883-14.3168
621.8740.62790.44231.08420.32211.3725-0.07670.13910.0407-0.52280.13570.0749-0.8059-0.6728-0.00082.8058-0.54440.5652.5463-0.36253.8137-20.8586-74.114122.2169
630.3920.3362-0.25340.3519-0.54110.8921-0.33320.0439-0.62320.31040.79420.93710.4414-0.2532-0.00031.41430.1298-0.02461.7190.08331.7385-17.3659-43.77637.0563
640.3038-0.09690.2920.14760.09130.5516-0.03880.108-0.4982-0.6324-1.4070.8805-0.8812-0.93170.05293.314-0.06510.21222.8698-0.64533.6155-14.5768-69.817314.5116
650.03490.0062-0.05040.0043-0.00670.07480.08370.1616-0.0113-0.28480.162-0.01650.0793-0.05430.01335.13031.3165-0.38374.0524-0.23522.7348-15.2221-73.48327.7678
660.10270.0745-0.21570.1725-0.08880.2345-0.3961-0.8793-0.51150.85970.50930.5630.8605-0.2526-0.00451.59430.1741-0.14471.80270.0941.3273-19.5944-40.11594.829
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 845 )
2X-RAY DIFFRACTION2chain 'A' and (resid 846 through 1454 )
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 171 )
4X-RAY DIFFRACTION4chain 'B' and (resid 172 through 242 )
5X-RAY DIFFRACTION5chain 'B' and (resid 243 through 370 )
6X-RAY DIFFRACTION6chain 'B' and (resid 371 through 538 )
7X-RAY DIFFRACTION7chain 'B' and (resid 539 through 744 )
8X-RAY DIFFRACTION8chain 'B' and (resid 745 through 1051 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1052 through 1224 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 26 )
11X-RAY DIFFRACTION11chain 'C' and (resid 27 through 51 )
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 163 )
13X-RAY DIFFRACTION13chain 'C' and (resid 164 through 209 )
14X-RAY DIFFRACTION14chain 'C' and (resid 210 through 267 )
15X-RAY DIFFRACTION15chain 'D' and (resid 3 through 23 )
16X-RAY DIFFRACTION16chain 'D' and (resid 24 through 133 )
17X-RAY DIFFRACTION17chain 'D' and (resid 134 through 203 )
18X-RAY DIFFRACTION18chain 'D' and (resid 204 through 221 )
19X-RAY DIFFRACTION19chain 'E' and (resid 4 through 89 )
20X-RAY DIFFRACTION20chain 'E' and (resid 90 through 130 )
21X-RAY DIFFRACTION21chain 'E' and (resid 131 through 215 )
22X-RAY DIFFRACTION22chain 'F' and (resid 69 through 78 )
23X-RAY DIFFRACTION23chain 'F' and (resid 79 through 86 )
24X-RAY DIFFRACTION24chain 'F' and (resid 87 through 102 )
25X-RAY DIFFRACTION25chain 'F' and (resid 103 through 116 )
26X-RAY DIFFRACTION26chain 'F' and (resid 117 through 126 )
27X-RAY DIFFRACTION27chain 'F' and (resid 127 through 132 )
28X-RAY DIFFRACTION28chain 'F' and (resid 133 through 142 )
29X-RAY DIFFRACTION29chain 'F' and (resid 143 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 155 )
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 13 )
32X-RAY DIFFRACTION32chain 'G' and (resid 14 through 34 )
33X-RAY DIFFRACTION33chain 'G' and (resid 35 through 79 )
34X-RAY DIFFRACTION34chain 'G' and (resid 80 through 151 )
35X-RAY DIFFRACTION35chain 'G' and (resid 152 through 171 )
36X-RAY DIFFRACTION36chain 'H' and (resid 2 through 43 )
37X-RAY DIFFRACTION37chain 'H' and (resid 44 through 81 )
38X-RAY DIFFRACTION38chain 'H' and (resid 82 through 91 )
39X-RAY DIFFRACTION39chain 'H' and (resid 92 through 101 )
40X-RAY DIFFRACTION40chain 'H' and (resid 102 through 110 )
41X-RAY DIFFRACTION41chain 'H' and (resid 111 through 127 )
42X-RAY DIFFRACTION42chain 'H' and (resid 128 through 140 )
43X-RAY DIFFRACTION43chain 'H' and (resid 141 through 146 )
44X-RAY DIFFRACTION44chain 'I' and (resid 2 through 52 )
45X-RAY DIFFRACTION45chain 'I' and (resid 53 through 115 )
46X-RAY DIFFRACTION46chain 'J' and (resid 1 through 17 )
47X-RAY DIFFRACTION47chain 'J' and (resid 18 through 31 )
48X-RAY DIFFRACTION48chain 'J' and (resid 32 through 55 )
49X-RAY DIFFRACTION49chain 'J' and (resid 56 through 65 )
50X-RAY DIFFRACTION50chain 'K' and (resid 1 through 18 )
51X-RAY DIFFRACTION51chain 'K' and (resid 19 through 39 )
52X-RAY DIFFRACTION52chain 'K' and (resid 40 through 62 )
53X-RAY DIFFRACTION53chain 'K' and (resid 63 through 82 )
54X-RAY DIFFRACTION54chain 'K' and (resid 83 through 109 )
55X-RAY DIFFRACTION55chain 'K' and (resid 110 through 114 )
56X-RAY DIFFRACTION56chain 'L' and (resid 27 through 31 )
57X-RAY DIFFRACTION57chain 'L' and (resid 32 through 36 )
58X-RAY DIFFRACTION58chain 'L' and (resid 37 through 46 )
59X-RAY DIFFRACTION59chain 'L' and (resid 47 through 51 )
60X-RAY DIFFRACTION60chain 'L' and (resid 52 through 58 )
61X-RAY DIFFRACTION61chain 'L' and (resid 59 through 70 )
62X-RAY DIFFRACTION62chain 'T' and (resid 10 through 14 )
63X-RAY DIFFRACTION63chain 'T' and (resid 15 through 28 )
64X-RAY DIFFRACTION64chain 'N' and (resid 1 through 5 )
65X-RAY DIFFRACTION65chain 'N' and (resid 6 through 7 )
66X-RAY DIFFRACTION66chain 'P' and (resid 1 through 10 )

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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