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- PDB-4f7u: The 6S snRNP assembly intermediate -

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基本情報

登録情報
データベース: PDB / ID: 4f7u
タイトルThe 6S snRNP assembly intermediate
要素
  • (Small nuclear ribonucleoprotein ...) x 5
  • Methylosome subunit pICln
キーワードSPLICING / Assembly Machine
機能・相同性
機能・相同性情報


SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / snRNP Assembly / mRNA Splicing - Minor Pathway / RNA Polymerase II Transcription Termination / mRNA Splicing - Major Pathway / U7 snRNP / U12-type spliceosomal complex / methylosome / U1 snRNP binding ...SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / snRNP Assembly / mRNA Splicing - Minor Pathway / RNA Polymerase II Transcription Termination / mRNA Splicing - Major Pathway / U7 snRNP / U12-type spliceosomal complex / methylosome / U1 snRNP binding / pICln-Sm protein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / cell volume homeostasis / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / chloride transport / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / cytoskeleton / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
ICln / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / Small nuclear ribonucleoprotein D1 / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 ...ICln / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / Small nuclear ribonucleoprotein D1 / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / SH3 type barrels. / PH-like domain superfamily / Roll / Mainly Beta
類似検索 - ドメイン・相同性
Methylosome subunit pICln / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein F
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Xenopus laevis (アフリカツメガエル)
Drosophila melanogaster (キイロショウジョウバエ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.898 Å
データ登録者Grimm, C. / Pelz, J.P.
引用ジャーナル: Mol Cell / 年: 2013
タイトル: Structural basis of assembly chaperone- mediated snRNP formation.
著者: Clemens Grimm / Ashwin Chari / Jann-Patrick Pelz / Jochen Kuper / Caroline Kisker / Kay Diederichs / Holger Stark / Hermann Schindelin / Utz Fischer /
要旨: Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step- ...Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit. This so-called 6S complex docks subsequently onto the SMN complex, which removes pICln and enables the transfer of pre-assembled Sm proteins onto snRNA. X-ray crystallography and electron microscopy was used to investigate the structural basis of snRNP assembly. The 6S complex structure identifies pICln as an Sm protein mimic, which enables the topological organization of the Sm pentamer in a closed ring. A second structure of 6S bound to the SMN complex components SMN and Gemin2 uncovers a plausible mechanism of pICln elimination and Sm protein activation for snRNA binding. Our studies reveal how assembly factors facilitate formation of RNA-protein complexes in vivo.
履歴
登録2012年5月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年1月30日Provider: repository / タイプ: Initial release
改定 1.12013年3月13日Group: Database references
改定 1.22015年1月28日Group: Structure summary
改定 1.32017年8月9日Group: Refinement description / Source and taxonomy / カテゴリ: entity_src_gen / software
Item: _entity_src_gen.entity_id / _entity_src_gen.gene_src_common_name ..._entity_src_gen.entity_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_src_id
改定 1.42023年9月13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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Small nuclear ribonucleoprotein Sm D1
B: Small nuclear ribonucleoprotein Sm D2
C: Small nuclear ribonucleoprotein Sm D1
D: Small nuclear ribonucleoprotein Sm D2
E: Small nuclear ribonucleoprotein E
H: Small nuclear ribonucleoprotein E
F: Small nuclear ribonucleoprotein F
I: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein G
J: Small nuclear ribonucleoprotein G
Q: Methylosome subunit pICln
P: Methylosome subunit pICln
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)141,45113
ポリマ－141,16812
非ポリマー2821
水6,702372
1
A: Small nuclear ribonucleoprotein Sm D1
B: Small nuclear ribonucleoprotein Sm D2
E: Small nuclear ribonucleoprotein E
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein G
P: Methylosome subunit pICln


分子量 (理論値)分子数
合計 (水以外)70,5846
ポリマ－70,5846
非ポリマー00
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-49 kcal/mol
Surface area21880 Å2
手法PISA
2
C: Small nuclear ribonucleoprotein Sm D1
D: Small nuclear ribonucleoprotein Sm D2
H: Small nuclear ribonucleoprotein E
I: Small nuclear ribonucleoprotein F
J: Small nuclear ribonucleoprotein G
Q: Methylosome subunit pICln
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,8667
ポリマ－70,5846
非ポリマー2821
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-52 kcal/mol
Surface area22430 Å2
手法PISA
単位格子
Length a, b, c (Å)180.720, 65.298, 99.346
Angle α, β, γ (deg.)90.00, 92.47, 90.00
Int Tables number5
Space group name H-MC121

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要素

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Small nuclear ribonucleoprotein ... , 5種, 10分子 ACBDEHFIGJ

#1: タンパク質 Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


分子量: 13310.653 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Snrpd1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62315
#2: タンパク質 Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


分子量: 13551.928 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Snrpd2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62317
#3: タンパク質 Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


分子量: 10817.601 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Snrpe / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62305
#4: タンパク質 Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


分子量: 9734.171 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
遺伝子: snrpf / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62321
#5: タンパク質 Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


分子量: 8508.084 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Snrpg / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62309

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タンパク質 , 1種, 2分子 QP

#6: タンパク質 Methylosome subunit pICln / SD10511p


分子量: 14661.660 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ)
遺伝子: CG4924, icln / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A1ZAW5

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非ポリマー , 2種, 373分子

#7: 化合物 ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / ヘキサエチレングリコ-ル


分子量: 282.331 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C12H26O7 / コメント: 沈殿剤*YM
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 372 / 由来タイプ: 天然 / 式: H2O

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詳細

配列の詳細THE SEQUENCE FOR CHAIN P AND Q (PICLN) MATCHES TO THE SEQEUNCE OF GENBANK ACCESSION NO AAF21126. ...THE SEQUENCE FOR CHAIN P AND Q (PICLN) MATCHES TO THE SEQEUNCE OF GENBANK ACCESSION NO AAF21126. THE MISMATCH TO UNP ACCESS A1ZAW5 AT POSITION 6 IS DUE TO POLYMORPHISM.

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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: 2.07 Å3/Da / 溶媒含有率: 40.7 %
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: 15% Jeffamine ED-2003 titrated to pH 7, 10% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: ESRF / ビームライン: ID14-4 / 波長: 0.9393 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年10月20日
放射モノクロメーター: XXX / 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: 0.9393 Å / 相対比: 1
反射解像度: 1.9→49.6 Å / Num. all: 91669 / Num. obs: 88058 / % possible obs: 96.2 % / 冗長度: 2.69 %
反射 シェル解像度: 1.9→2.01 Å / 冗長度: 2.71 % / Rsym value: 0.582 / % possible all: 96.2

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解析

ソフトウェア
名称バージョン分類
MxCuBEデータ収集
PHASER位相決定
PHENIXphenix.refine: 1.7.1_743精密化
XDSデータ削減
XDS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: 4F77

4f77
PDB 未公開エントリ


解像度: 1.898→49.627 Å / SU ML: 0.5 / σ(F): 1.99 / 位相誤差: 23.5 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2213 4426 5.03 %
Rwork0.1807 --
obs0.1827 88054 96.06 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 47.437 Å2 / ksol: 0.348 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--6.4478 Å20 Å2-3.0352 Å2
2--8.7345 Å2-0 Å2
3----2.2867 Å2
精密化ステップサイクル: LAST / 解像度: 1.898→49.627 Å
タンパク質核酸リガンド溶媒全体
原子数7985 0 13 372 8370
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0158301
X-RAY DIFFRACTIONf_angle_d1.58311217
X-RAY DIFFRACTIONf_dihedral_angle_d14.623195
X-RAY DIFFRACTIONf_chiral_restr0.1141296
X-RAY DIFFRACTIONf_plane_restr0.0081414
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8982-1.91980.35021170.31282518X-RAY DIFFRACTION85
1.9198-1.94240.36691610.29782697X-RAY DIFFRACTION96
1.9424-1.96610.321470.26382777X-RAY DIFFRACTION96
1.9661-1.9910.27191510.24312782X-RAY DIFFRACTION96
1.991-2.01720.25441550.22812724X-RAY DIFFRACTION96
2.0172-2.04480.26841320.22392830X-RAY DIFFRACTION96
2.0448-2.0740.24291270.21992780X-RAY DIFFRACTION96
2.074-2.1050.26821370.21552795X-RAY DIFFRACTION96
2.105-2.13790.26561510.20182762X-RAY DIFFRACTION97
2.1379-2.17290.23381410.22786X-RAY DIFFRACTION96
2.1729-2.21040.22471580.19132768X-RAY DIFFRACTION97
2.2104-2.25060.27711490.19492823X-RAY DIFFRACTION97
2.2506-2.29390.22741660.1912754X-RAY DIFFRACTION97
2.2939-2.34070.27571420.19472837X-RAY DIFFRACTION97
2.3407-2.39160.27611460.1942763X-RAY DIFFRACTION97
2.3916-2.44720.22361360.18492823X-RAY DIFFRACTION97
2.4472-2.50840.26811500.19052813X-RAY DIFFRACTION97
2.5084-2.57620.23911590.19422775X-RAY DIFFRACTION97
2.5762-2.6520.26851410.19092831X-RAY DIFFRACTION97
2.652-2.73760.25641650.18792801X-RAY DIFFRACTION97
2.7376-2.83550.23211630.18482841X-RAY DIFFRACTION98
2.8355-2.9490.25861660.19052767X-RAY DIFFRACTION97
2.949-3.08320.21861370.19472853X-RAY DIFFRACTION97
3.0832-3.24570.2381300.18732815X-RAY DIFFRACTION97
3.2457-3.4490.20891710.17962798X-RAY DIFFRACTION96
3.449-3.71520.18181430.16512819X-RAY DIFFRACTION96
3.7152-4.08890.18591490.15312801X-RAY DIFFRACTION96
4.0889-4.68020.15041530.12352811X-RAY DIFFRACTION96
4.6802-5.89510.17961380.14782889X-RAY DIFFRACTION97
5.8951-49.64380.23211450.20142795X-RAY DIFFRACTION92
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)
10.1266-0.028-0.01180.0639-0.05840.0593-0.10720.05660.4084-0.08580.08270.0683-0.026-0.1756-0.03870.32890.0283-0.0220.19680.03760.3793-6.34596.475925.6601
20.5969-0.52310.01350.72020.00030.05370.0751-0.51390.2951-0.0789-0.0961-0.15390.1353-0.2414-0.02590.2303-0.0338-0.00740.3564-0.02230.1463-6.7184-2.394734.7237
30.3503-0.0748-0.03310.05020.01520.03120.1282-0.06630.55820.1370.03670.00370.1267-0.15390.05590.27620.08750.02710.04860.02770.4979-11.30238.398925.1067
40.02060.0105-0.00840.008-0.01040.02440.00940.12080.1342-0.07350.09710.0862-0.1228-0.08690.10190.39220.16340.02040.48180.39230.4828-18.1655.98845.5321
50.05580.0133-0.01820.08780.03340.0263-0.01890.07440.43060.16030.00690.07980.0758-0.036-0.01330.39940.12920.00740.3090.08430.2868-24.14811.011619.1082
60.06110.03120.07660.01890.01730.1305-0.06060.04620.2538-0.0271-0.03370.0051-0.1409-0.0482-0.0720.18140.30740.01950.07940.24640.3444-21.70245.637119.5733
70.00330.00010.00410.0106-0.00020.00180.0820.04620.0644-0.0740.077-0.1122-0.02140.0542-00.29670.05710.00020.2930.07760.2855-10.40081.289112.7108
80.08280.1150.12250.19980.27560.3783-0.0278-0.0630.35520.1137-0.0840.08730.0854-0.2398-0.05880.34160.14170.04450.27110.03070.3887-23.12314.910624.9354
90.00580.0039-0.0042-0.003-0.00170.00130.1045-0.11320.17930.16640.00190.13280.1022-0.336700.4906-0.02260.11690.503-0.0710.4093-28.85650.174131.7363
100.1297-0.0303-0.00980.0438-0.07450.1611-0.02660.17490.29750.1030.07440.20860.1709-0.18630.0770.24420.0754-0.01510.28090.0670.3013-20.61861.481418.5446
110.002-0.004700.0057-0.00050.0005-0.1388-0.0233-0.1202-0.1426-0.05980.2043-0.0282-0.133-00.2842-0.0038-0.0120.33170.0110.340225.0828-19.260239.3988
120.00330.00410.00280.01120.0160.0146-0.1482-0.3063-0.21760.14130.07010.0795-0.0101-0.064900.2614-0.01560.00910.47670.01070.26930.8632-10.601947.6836
130.00290.02150.00620.04480.00630.0003-0.049-0.3132-0.16640.07790.04680.0887-0.13640.149100.34-0.05410.0250.4799-0.08880.283131.1873-6.225645.5572
140.0574-0.0211-0.01540.24210.04320.04170.0765-0.39470.16280.0317-0.0121-0.0076-0.04420.23510.07020.2553-0.0374-0.02860.4507-0.1460.307631.0705-2.707845.6165
150.00880.03110.02080.10840.01950.210.0608-0.26360.2814-0.01510.01560.1832-0.0927-0.12320.0390.2491-0.0150.00610.368-0.13970.292826.4761-0.308546.8151
160.0055-0.00380.00370.00530.00250.00220.0723-0.3146-0.1125-0.0747-0.1099-0.1536-0.08070.1839-00.2546-0.0048-0.00680.32740.02230.221634.9139-9.142439.8646
170.0420.01750.02920.05420.00680.0438-0.0928-0.1141-0.12590.2218-0.1266-0.04110.0655-0.0091-0.06780.3871-0.0660.08350.43280.15040.353229.2617-24.415646.5078
180.00670.00210.0058-0.00020.0033-0.0006-0.14320.0106-0.0393-0.0059-0.14910.0383-0.0149-0.089400.5194-0.0257-0.05290.6281-0.32760.68731.3976-29.817623.6912
190.0154-0.0212-0.01370.02250.0170.0103-0.05730.0264-0.3662-0.01870.0289-0.12140.096-0.017-0.00820.4470.10090.0520.24090.04960.489641.1494-28.587730.6825
200.02810.0130.05430.00490.02330.0931-0.2012-0.192-0.04690.019-0.01270.0002-0.1420.32820.00540.37070.114-0.03390.3470.06760.341346.2236-16.675436.4114
210.2941-0.2373-0.2380.31970.30260.2706-0.1622-0.1459-0.22260.1163-0.03890.1570.18560.1914-0.13930.26770.08850.01390.38630.15190.348342.1628-20.995338.8603
220.0157-0.00040.00890.01030.00650.0084-0.0267-0.0123-0.0994-0.07360.0042-0.0019-0.0445-0.0706-00.33060.0594-0.01790.2536-0.00640.327432.2446-18.734329.7444
230.0114-0.0157-0.01590.00450.01050.0137-0.0976-0.1895-0.13960.07780.0741-0.0709-0.01010.312200.31790.0765-0.01440.44820.08910.366643.9019-17.915743.1622
240.058-0.0577-0.00810.0950.07230.063-0.087-0.2476-0.20960.26650.0568-0.1016-0.25490.50850.04660.28360.0367-0.06280.58340.08580.265644.8767-13.736344.7374
250.4356-0.06360.41420.1747-0.00050.4184-0.2636-0.0759-0.0783-0.158-0.0734-0.1630.0050.1976-0.07340.2690.12150.12060.31950.04460.331745.742-18.120332.3478
260.02670.0081-0.0120.02250.02980.02750.07470.13550.0611-0.0189-0.1182-0.1203-0.01160.0227-0.0450.05780.45560.58871.0672-0.1443-0.5951-2.3531-30.74533.5033
270.0159-0.01140.0035-0.0028-0.0070.00610.06930.32180.0105-0.1967-0.22120.1471-0.05560.187100.25740.0793-0.0170.3173-0.06310.2139-15.2402-30.72688.2258
280.0899-0.05430.0630.2652-0.00720.0260.15770.24160.26550.1077-0.21350.02490.04070.1963-0.00080.22220.04010.02270.39870.01810.2266-14.2499-23.49269.4879
290.0749-0.04070.04630.0527-0.04090.0180.25340.0527-0.2479-0.1844-0.18640.21640.28410.072-0.00210.2712-0.0368-0.00110.3604-0.00030.2468-24.6269-28.49589.1975
300.0184-0.01980.03390.0167-0.02490.01780.11160.40520.0576-0.0585-0.0612-0.13510.0209-0.021200.23110.0519-0.00030.34130.02290.2205-13.9987-24.42589.2074
310.01610.0031-0.00740.01020.01310.0074-0.26270.2093-0.036-0.30010.02-0.0123-0.01730.0856-0.00140.3375-0.0114-0.09540.4138-0.06820.319431.38422.22512.9957
320.0958-0.0547-0.03790.06350.00430.020.07380.01250.06060.01850.31960.009-0.12030.077100.2979-0.07130.00810.3165-0.04220.251844.213.040113.8342
330.0439-0.04680.0150.0343-0.00790.0209-0.00190.10320.0957-0.090.07710.07270.0052-0.034600.2608-0.0685-0.0130.3187-0.02420.255539.8143-3.611610.1991
340.0441-0.00860.01190.0311-0.03210.01440.00390.21570.1067-0.17160.0059-0.0597-0.15720.064900.2724-0.06580.00970.3066-0.04920.287452.1082-0.06610.8457
350.0487-0.0079-0.01330.03190.0260.0023-0.07420.22140.02410.00050.12270.026-0.1252-0.009200.3195-0.05420.00040.2572-0.01940.252541.4316-0.497511.9683
360.26560.01750.05880.25990.3310.4624-0.32540.17750.1523-0.1041-0.2006-0.073-0.21720.1403-0.44730.2270.05640.04420.47910.16620.188-19.8574-14.2016-0.1617
37-0.0021-0.02140.05320.17490.05110.077-0.01560.10.1028-0.2006-0.06680.09250.02720.103400.31850.0797-0.01950.410.07030.3048-24.2986-8.87047.8921
380.12050.01140.00720.22750.0020.0942-0.13080.26340.067-0.0117-0.10450.181-0.0363-0.0817-0.04940.2190.09120.00480.32890.02450.2524-26.2969-11.217410.1493
390.03950.00710.00640.01930.01330.028-0.09460.2151-0.0524-0.1632-0.04560.1824-0.0058-0.23820.00660.3693-0.06620.01090.3106-0.15430.277739.5871-15.51677.1623
400.0899-0.04630.14060.025-0.07640.2349-0.27680.1271-0.1317-0.0661-0.1418-0.0501-0.0368-0.1229-0.26280.35180.06090.07010.1691-0.09720.266849.9995-15.917515.8952
410.0036-0.0050.00930.0745-0.11420.1483-0.11220.0841-0.21980.0406-0.1245-0.1549-0.04050.1031-0.01480.34880.05730.05630.2359-0.02940.372849.3554-14.707321.1198
420.02040.0066-0.01970.0314-0.09430.1454-0.3513-0.1305-0.0430.00490.1095-0.20540.22520.1955-0.00870.30020.0993-0.00260.3553-0.01890.454750.7718-16.328822.5321
430.11220.14510.11660.18010.11740.0975-0.2801-0.1131-0.1363-0.10390.0117-0.08020.2150.2274-0.05470.29950.09010.06970.22320.00610.263248.3603-14.919221.0199
440.0034-0.00290.00120.001-0.00090.00120.0696-0.01690.0457-0.06570.0816-0.1481-0.04790.0642-00.27620.0355-0.02730.4564-0.01730.4679.2023-27.975120.9856
450.01810.01160.04460.00390.0150.05510.12410.03860.10660.1878-0.1737-0.18820.20760.2199-00.33760.0715-0.00270.25170.0030.3035-3.1332-31.421823.3527
460.1590.12910.04180.22070.11480.080.19970.0971-0.07410.1539-0.07030.20180.31480.1328-0.00010.37470.0784-0.02020.23350.02140.2399-3.1495-33.271820.1699
470.00340.0043-0.00420.0056-0.00360.0107-0.01530.04190.0458-0.0108-0.03650.0102-0.0556-0.006500.3360.06160.07280.74710.29110.6231.7278-21.754713.4603
480.00650.01710.0010.0149-0.0109-0.00260.26660.2001-0.30940.1274-0.04180.24990.32990.199400.44440.1093-0.01630.2302-0.00940.3655-5.7237-36.386718.0512
490.0251-0.02810.02390.0365-0.02430.02390.0926-0.0231-0.004-0.02110.05170.02280.0219-0.06530.00770.5802-0.16520.12270.3660.11950.9525-17.52-38.758926.8941
50-0.00250.0036-0.00130.0011-0.0001-0.00020.06610.0422-0.14380.0264-0.01180.16480.0666-0.01950.03440.71080.0137-0.1626-0.0011-0.08970.571-11.5219-40.574618.552
510.012-0.00580.0140.0062-0.00380.0034-0.03970.18870.22260.0552-0.11270.06550.11220.1485-00.28970.0846-0.0370.27960.01670.2525-5.5108-29.55113.2578
520.02140.02520.02720.01710.01080.00330.07750.03050.08740.2526-0.04140.22830.17040.081-00.3556-0.0055-0.05560.2991-0.00420.2723-1.5621-28.956425.6542
530.0039-0.0023-0.00210.00040.00380.001-0.00610.0048-0.0556-0.0873-0.0860.1628-0.0792-0.055400.43520.1486-0.02360.46530.10930.929821.189213.761716.0535
540.0048-0.0048-0.00560.00580.00970.01460.0834-0.1324-0.01860.01140.0103-0.1076-0.07530.1275-00.4943-0.0220.09690.2540.0220.334135.368713.844421.1686
550.0506-0.0037-0.0302-0.0030.0230.05430.26930.1330.24520.0863-0.08250.079-0.4219-0.10340.01260.44070.0457-0.00410.20010.02450.501232.584713.873515.4113
560.0142-0.0123-0.00830.01720.01430.00950.0317-0.0312-0.06690.0289-0.0990.12130.0084-0.27600.35640.027-0.00420.4579-0.00450.450127.91825.145313.718
570.2292-0.04990.10640.061-0.05060.08040.1106-0.00280.0231-0.0319-0.03850.016-0.09580.04670.01820.528-0.11710.03460.24190.09450.604742.555419.094515.474
580.00070.00170.00120.0076-0.00560.00350.22360.04890.2022-0.0920.0863-0.0752-0.08570.0545-00.649-0.04490.08240.34620.09190.444240.343316.23359.5326
590.04770.0128-0.0308-0.0003-0.00810.0115-0.0339-0.02220.18550.1555-0.13050.2644-0.33890.2309-00.40650.0290.0640.2248-0.00940.455331.508511.351919.8602
600.00230.00160.00090.06330.0036-0.00290.26550.03340.07660.07130.12870.1778-0.0032-0.16660.15590.38610.07090.20880.07440.1710.800518.393213.588826.4254
610.0147-0.02020.03110.4498-0.55890.7260.38270.06260.24710.23720.28420.2526-0.434-0.31250.35080.4410.02640.22420.2424-0.06740.678719.350215.350939.4622
620.101-0.1575-0.15650.65390.06680.55660.2503-0.4260.8086-0.23510.2554-0.3518-0.28320.51950.57060.383-0.09510.1740.1304-0.18620.572925.852711.668138.3416
630.04370.03790.01980.03640.00130.0099-0.02020.11730.1267-0.08320.23940.120.0193-0.09040.00010.2311-0.00780.03720.283-0.04850.313316.86311.487138.7542
640.0068-0.00730.00910.0033-0.00580.01090.06870.03670.08290.07090.15680.070.07120.0951-0.00010.3377-0.0497-0.05240.2831-0.01120.28222.7889-25.478528.2384
650.00770.0018-0.00750.00040.00290.00630.21550.14940.0288-0.17540.1805-0.0631-0.16180.114500.34480.0778-0.06560.5014-0.06790.40315.5651-22.089228.3172
660.0044-0.00160.00250.003-0.00280.0018-0.0039-0.09190.05950.03310.0361-0.1045-0.07420.03100.296-0.03390.00310.273-0.02790.359415.3393-12.595633.5168
670.00040.00450.00940.0330.01240.0291-0.0421-0.08360.02150.32350.1025-0.01440.0641-0.01810.01020.2894-0.0133-0.05480.47530.08340.2424.5045-18.462643.9207
680.1076-0.0148-0.0271.05290.85590.73120.0812-0.0921-0.2838-0.11770.3511-0.11040.15550.09870.30830.23220.0036-0.06890.23540.05330.23258.4523-19.54535.9859
690.0658-0.0450.01190.0931-0.04220.0206-0.0209-0.072-0.02340.03790.03720.0410.05560.02430.02090.58140.0951-0.29250.15740.22230.59668.8614-29.495540.3403
700.0481-0.02750.02350.1352-0.00360.00240.055-0.2853-0.1832-0.10050.04670.10630.0314-0.09060.00010.2335-0.00510.00040.29230.030.23511.1524-11.137338.5307
710.00770.0083-0.0030.0032-0.00780.00740.1937-0.0048-0.20640.1811-0.19450.22470.3428-0.317800.4829-0.1276-0.07070.52910.0350.4575-6.1815-23.777435.4055
720.0491-0.0121-0.03050.1230.00220.0232-0.0332-0.0615-0.14550.05970.1125-0.2910.11260.07240.00340.2474-0.0208-0.04610.43220.03990.24363.2558-13.906443.1316
730.0305-0.0093-0.02010.0647-0.03490.01830.135-0.0868-0.0167-0.1751-0.0685-0.07740.05660.10120.00140.2078-0.0061-0.00490.2121-0.00730.22458.0581-6.642633.1633
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1001:1019)
2X-RAY DIFFRACTION2chain 'A' and (resseq 1020:1061)
3X-RAY DIFFRACTION3chain 'A' and (resseq 1062:1082)
4X-RAY DIFFRACTION4chain 'B' and (resseq 2022:2037)
5X-RAY DIFFRACTION5chain 'B' and (resseq 2038:2049)
6X-RAY DIFFRACTION6chain 'B' and (resseq 2050:2059)
7X-RAY DIFFRACTION7chain 'B' and (resseq 2060:2064)
8X-RAY DIFFRACTION8chain 'B' and (resseq 2065:2074)
9X-RAY DIFFRACTION9chain 'B' and (resseq 2075:2096)
10X-RAY DIFFRACTION10chain 'B' and (resseq 2097:2114)
11X-RAY DIFFRACTION11chain 'C' and (resseq 1002:1010)
12X-RAY DIFFRACTION12chain 'C' and (resseq 1011:1019)
13X-RAY DIFFRACTION13chain 'C' and (resseq 1020:1032)
14X-RAY DIFFRACTION14chain 'C' and (resseq 1033:1052)
15X-RAY DIFFRACTION15chain 'C' and (resseq 1053:1061)
16X-RAY DIFFRACTION16chain 'C' and (resseq 1062:1069)
17X-RAY DIFFRACTION17chain 'C' and (resseq 1070:1082)
18X-RAY DIFFRACTION18chain 'D' and (resseq 2016:2026)
19X-RAY DIFFRACTION19chain 'D' and (resseq 2027:2038)
20X-RAY DIFFRACTION20chain 'D' and (resseq 2039:2049)
21X-RAY DIFFRACTION21chain 'D' and (resseq 2050:2059)
22X-RAY DIFFRACTION22chain 'D' and (resseq 2060:2064)
23X-RAY DIFFRACTION23chain 'D' and (resseq 2065:2074)
24X-RAY DIFFRACTION24chain 'D' and (resseq 2075:2102)
25X-RAY DIFFRACTION25chain 'D' and (resseq 2103:2113)
26X-RAY DIFFRACTION26chain 'E' and (resseq 3013:3027)
27X-RAY DIFFRACTION27chain 'E' and (resseq 3028:3035)
28X-RAY DIFFRACTION28chain 'E' and (resseq 3036:3055)
29X-RAY DIFFRACTION29chain 'E' and (resseq 3056:3075)
30X-RAY DIFFRACTION30chain 'E' and (resseq 3076:3090)
31X-RAY DIFFRACTION31chain 'H' and (resseq 3014:3027)
32X-RAY DIFFRACTION32chain 'H' and (resseq 3028:3040)
33X-RAY DIFFRACTION33chain 'H' and (resseq 3041:3055)
34X-RAY DIFFRACTION34chain 'H' and (resseq 3056:3075)
35X-RAY DIFFRACTION35chain 'H' and (resseq 3076:3091)
36X-RAY DIFFRACTION36chain 'F' and (resseq 4004:4023)
37X-RAY DIFFRACTION37chain 'F' and (resseq 4024:4050)
38X-RAY DIFFRACTION38chain 'F' and (resseq 4051:4076)
39X-RAY DIFFRACTION39chain 'I' and (resseq 4003:4014)
40X-RAY DIFFRACTION40chain 'I' and (resseq 4015:4023)
41X-RAY DIFFRACTION41chain 'I' and (resseq 4024:4036)
42X-RAY DIFFRACTION42chain 'I' and (resseq 4037:4056)
43X-RAY DIFFRACTION43chain 'I' and (resseq 4057:4076)
44X-RAY DIFFRACTION44chain 'G' and (resseq 5007:5012)
45X-RAY DIFFRACTION45chain 'G' and (resseq 5013:5024)
46X-RAY DIFFRACTION46chain 'G' and (resseq 5025:5034)
47X-RAY DIFFRACTION47chain 'G' and (resseq 5035:5039)
48X-RAY DIFFRACTION48chain 'G' and (resseq 5040:5048)
49X-RAY DIFFRACTION49chain 'G' and (resseq 5049:5053)
50X-RAY DIFFRACTION50chain 'G' and (resseq 5054:5058)
51X-RAY DIFFRACTION51chain 'G' and (resseq 5059:5063)
52X-RAY DIFFRACTION52chain 'G' and (resseq 5064:5074)
53X-RAY DIFFRACTION53chain 'J' and (resseq 5008:5015)
54X-RAY DIFFRACTION54chain 'J' and (resseq 5016:5024)
55X-RAY DIFFRACTION55chain 'J' and (resseq 5025:5034)
56X-RAY DIFFRACTION56chain 'J' and (resseq 5035:5043)
57X-RAY DIFFRACTION57chain 'J' and (resseq 5044:5053)
58X-RAY DIFFRACTION58chain 'J' and (resseq 5054:5059)
59X-RAY DIFFRACTION59chain 'J' and (resseq 5060:5074)
60X-RAY DIFFRACTION60chain 'Q' and (resseq 6001:6013)
61X-RAY DIFFRACTION61chain 'Q' and (resseq 6014:6038)
62X-RAY DIFFRACTION62chain 'Q' and (resseq 6039:6142)
63X-RAY DIFFRACTION63chain 'Q' and (resseq 6143:6162)
64X-RAY DIFFRACTION64chain 'P' and (resseq 6001:6005)
65X-RAY DIFFRACTION65chain 'P' and (resseq 6006:6013)
66X-RAY DIFFRACTION66chain 'P' and (resseq 6014:6018)
67X-RAY DIFFRACTION67chain 'P' and (resseq 6019:6027)
68X-RAY DIFFRACTION68chain 'P' and (resseq 6028:6046)
69X-RAY DIFFRACTION69chain 'P' and (resseq 6047:6051)
70X-RAY DIFFRACTION70chain 'P' and (resseq 6052:6077)
71X-RAY DIFFRACTION71chain 'P' and (resseq 6078:6133)
72X-RAY DIFFRACTION72chain 'P' and (resseq 6134:6142)
73X-RAY DIFFRACTION73chain 'P' and (resseq 6143:6160)

+
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

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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