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- PDB-3szm: STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN C... -

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基本情報

登録情報
データベース: PDB / ID: 3szm
タイトルSTRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE
要素
  • Histone H2A.x
  • Microcephalin
キーワードCELL CYCLE/Peptide / DNA REPAIR / CELL CYCLE-Peptide complex
機能・相同性
機能・相同性情報


regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage ...regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / DNA damage checkpoint signaling / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / condensed nuclear chromosome / replication fork / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / meiotic cell cycle / Defective pyroptosis / male germ cell nucleus / double-strand break repair via homologous recombination / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / bone development / cerebral cortex development / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / site of double-strand break / heterochromatin formation / double-strand break repair / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / nucleosome assembly / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of inflammatory response / Oxidative Stress Induced Senescence / spermatogenesis / histone binding / damaged DNA binding / Estrogen-dependent gene expression / nuclear speck / Amyloid fiber formation / protein heterodimerization activity / centrosome / DNA damage response / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm
類似検索 - 分子機能
Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Histone H2AX / Microcephalin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.63 Å
データ登録者Singh, N. / Thompson, J.R. / Mer, G.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2012
タイトル: Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1.
著者: Singh, N. / Basnet, H. / Wiltshire, T.D. / Mohammad, D.H. / Thompson, J.R. / Heroux, A. / Botuyan, M.V. / Yaffe, M.B. / Couch, F.J. / Rosenfeld, M.G. / Mer, G.
履歴
登録2011年7月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02011年11月30日Provider: repository / タイプ: Initial release
改定 1.12012年8月29日Group: Database references
改定 1.22012年9月19日Group: Database references
改定 1.32024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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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: Microcephalin
B: Microcephalin
C: Microcephalin
D: Microcephalin
E: Microcephalin
F: Microcephalin
G: Microcephalin
H: Microcephalin
I: Histone H2A.x
J: Histone H2A.x
K: Histone H2A.x
L: Histone H2A.x
M: Histone H2A.x
N: Histone H2A.x
O: Histone H2A.x
P: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)185,47816
ポリマ－185,47816
非ポリマー00
水7,062392
1
A: Microcephalin
I: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-6 kcal/mol
Surface area10390 Å2
手法PISA
2
B: Microcephalin
J: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area10290 Å2
手法PISA
3
C: Microcephalin
K: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-7 kcal/mol
Surface area10700 Å2
手法PISA
4
D: Microcephalin
L: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area10510 Å2
手法PISA
5
E: Microcephalin
M: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-5 kcal/mol
Surface area10370 Å2
手法PISA
6
F: Microcephalin
N: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area10520 Å2
手法PISA
7
G: Microcephalin
O: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-6 kcal/mol
Surface area10760 Å2
手法PISA
8
H: Microcephalin
P: Histone H2A.x


分子量 (理論値)分子数
合計 (水以外)23,1852
ポリマ－23,1852
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-6 kcal/mol
Surface area10440 Å2
手法PISA
単位格子
Length a, b, c (Å)67.810, 82.230, 104.420
Angle α, β, γ (deg.)72.10, 89.87, 80.94
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Microcephalin


分子量: 21949.551 Da / 分子数: 8 / 断片: C-TERMINAL TANDEM BRCT DOMAINS, RESIDUES 640-835 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MCPH1 / プラスミド: PTEV / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 ROSETTA (DE3) / 参照: UniProt: Q8NEM0
#2: タンパク質・ペプチド
Histone H2A.x / H2a/x


分子量: 1235.236 Da / 分子数: 8 / 断片: C-TERMINAL FRAGMENT, RESIDUES 134-143 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P16104
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 392 / 由来タイプ: 天然 / 式: H2O
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

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試料調製

結晶マシュー密度: 2.95 Å3/Da / 溶媒含有率: 58.25 %
結晶化手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.8
詳細: 20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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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: APS / ビームライン: 19-ID / 波長: 1.0079 / 波長: 1.0079 Å
検出器検出器: CCD / 日付: 2007年2月15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: 1.0079 Å / 相対比: 1
反射解像度: 2.63→50 Å / Num. obs: 59208 / % possible obs: 90.2 % / 冗長度: 2.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.57
反射 シェル解像度: 2.63→2.74 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
直接法モデル構築
PHENIX(PHENIX.REFINE: 1.6.1_357)精密化
HKL-2000データ削減
HKL-2000データスケーリング
直接法位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.63→31.37 Å / SU ML: 0.4 / σ(F): 1.96 / 位相誤差: 26.08 / 立体化学のターゲット値: ML / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射
Rfree0.252 572 1.01 %
Rwork0.201 --
obs0.202 56418 89.7 %
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: 47.43 Å2 / ksol: 0.38 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1-1.2894 Å21.4388 Å20.4417 Å2
2--0.9267 Å20.0837 Å2
3----2.216 Å2
精密化ステップサイクル: LAST / 解像度: 2.63→31.37 Å
タンパク質核酸リガンド溶媒全体
原子数12173 0 0 392 12565
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00912578
X-RAY DIFFRACTIONf_angle_d1.04617169
X-RAY DIFFRACTIONf_dihedral_angle_d10.8044620
X-RAY DIFFRACTIONf_chiral_restr0.0531957
X-RAY DIFFRACTIONf_plane_restr0.0062140
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.89450.32641630.279714911X-RAY DIFFRACTION96
2.8945-3.31290.28161500.229315311X-RAY DIFFRACTION98
3.3129-4.17240.22821110.188110325X-RAY DIFFRACTION66
4.1724-31.36780.22131480.170715299X-RAY DIFFRACTION98
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)
11.27621.3202-0.40371.5836-0.98020.9210.07020.87530.2244-0.04270.2816-0.17490.04-0.7845-0.29420.40020.02010.09680.6707-0.00940.305913.187512.841775.1003
21.2713-0.04721.18371.51020.18441.06370.09640.53850.2079-0.29370.20630.24980.0144-0.7531-0.19050.3720.0230.070.79340.18310.393412.353318.829475.8766
31.30210.4459-1.74810.5614-1.31981.47090.6003-0.0054-0.07560.2977-0.3206-0.0894-0.1938-0.1275-0.19030.3954-0.05120.16220.34930.00370.1617.697117.259184.3016
41.07731.6298-0.30992.780.59593.48661.12540.23610.6983-0.0771-0.36590.9328-1.1030.2861-0.97760.6659-0.0130.50360.1478-0.00640.628420.905231.591285.7281
51.92920.29370.09910.20980.08280.00560.9813-0.16410.96990.6131-0.3067-0.4308-0.23250.2965-0.42740.8264-0.04640.46820.1272-0.0140.408134.983436.190276.4016
66.1936-0.59040.18772.62141.5110.98740.53160.50410.06910.4824-0.47320.2742-0.04760.2956-0.2070.40760.03710.13080.27730.05490.266936.081924.532865.5095
75.2222-0.1999-2.81830.1433-0.50996.17450.71090.42030.4769-0.42020.23910.4783-1.0617-0.5499-1.02640.39540.15450.32280.21510.09420.352829.786730.554471.9443
80.58390.37740.75160.21420.19040.9459-0.04120.15960.52530.69810.140.8174-0.5058-0.1711-0.21090.56650.07460.24230.19260.07590.549842.512934.178466.4205
91.004-0.84580.010.84520.10890.43040.4570.03950.26480.6147-0.068-0.46230.1297-0.0519-0.15370.4663-0.08180.08860.2461-0.01210.56341.884628.392576.1008
103.51870.0112-2.43886.82960.70169.57450.3188-0.3589-0.4719-0.0032-1.18870.9385-0.86191.10660.46530.4799-0.1868-0.08080.18480.19150.218745.932725.94779.5705
111.47351.1679-0.86791.4205-0.5331.9567-0.08060.2957-0.975-0.2041.0083-0.15170.5968-0.4116-0.57990.38140.0131-0.15130.3214-0.2150.350211.24662.039131.3571
123.58151.3646-0.38642.7494-0.0691.2317-0.13120.1862-0.8599-0.47680.449-0.79220.69930.3244-0.43420.45570.1956-0.15270.3078-0.22030.493915.793659.075633.5103
132.22970.91171.24060.94781.22930.90120.65180.02260.03690.3791-0.12130.03580.70560.1756-0.41580.4971-0.0643-0.15720.3257-0.0290.32978.656565.302339.8286
141.05360.6330.21970.8168-0.46132.78541.6824-0.76780.3519-0.8689-0.5318-0.11750.7474-0.2542-0.42710.4562-0.3534-0.39110.34970.08690.05623.42855.657948.9648
151.1857-0.4226-0.9443.3343-2.09172.5360.635-0.5389-0.45350.72160.37010.14610.1159-0.007-0.49921.0369-0.4387-0.42270.57720.42610.495-11.019145.999545.1358
161.4955-0.01240.33250.62420.34020.27191.2531-0.1767-1.2308-0.3487-0.1260.1180.5776-0.3749-0.61260.8457-0.2168-0.5110.15190.03510.5347-10.310648.497429.767
170.07270.09820.2050.56370.84981.36610.33150.2733-0.7317-0.7230.0325-0.16391.7722-0.4576-1.00731.1493-0.1599-0.67620.13320.13830.5874-4.023747.485638.7802
181.7215-1.07460.4510.80150.03943.09790.1444-0.0327-0.7917-0.2018-0.16950.46011.4381-0.3662-0.48991.261-0.3228-0.59640.19340.30170.6808-15.943539.322538.4918
191.28030.98720.64170.86540.5190.35540.3264-0.51290.63170.9412-0.6508-0.3039-0.816-0.1967-0.01070.7413-0.2535-0.44030.36060.23680.44-21.586345.405931.4855
201.94550.9663-0.09190.5998-0.04060.31540.924-0.1351-0.28940.0765-0.0599-0.22190.170.1483-0.39190.624-0.2714-0.14250.22450.24790.25-17.209353.722541.1123
210.498-0.3939-0.74961.6834-0.73221.0998-0.12160.0777-0.04730.42990.27780.0977-0.3109-0.2702-0.17810.20680.10140.00550.4424-0.04990.35049.59973.842518.2814
220.46930.6373-0.22181.2125-0.15520.7296-0.82010.44010.1117-0.20270.87980.4145-0.2732-0.4713-0.17260.03260.0320.08640.6429-0.15870.24673.0909-3.81720.6899
230.8374-0.95820.83251.99660.04841.8056-0.29940.85050.0278-0.0770.3093-0.25850.1780.57420.00690.16440.13740.00490.45870.02550.434912.98335.91214.6626
241.63840.1097-0.94921.8513-0.04151.2377-0.02330.00460.24420.1393-0.0087-0.20280.01940.00080.01380.21540.037-0.02640.4281-0.08650.248711.81353.121226.4742
250.6706-0.53150.44521.9411-0.65690.9969-0.0442-0.35890.57670.4861-0.214-0.2254-0.24130.161-0.02970.28280.03370.00080.5564-0.11460.322511.40415.224133.157
264.56291.2293-2.72382.39081.25324.32581.1781-0.47430.8642-0.4898-0.4399-0.0156-0.59010.2082-0.54750.36960.17180.19220.256-0.12520.423815.228918.021728.4811
270.02380.1193-0.0382.0086-0.84791.08140.5116-0.03520.87650.13680.0506-0.771-0.62460.0343-0.31210.6048-0.03530.1920.3332-0.0450.807529.947621.585722.8783
283.3026-1.1681-1.47651.07041.38241.91850.2353-0.54240.352-0.52670.23190.1388-0.02490.1187-0.29510.1564-0.05090.1060.22550.05010.420930.590711.223815.6738
292.9201-1.2316-0.42091.26460.66260.30620.20570.12811.8195-1.08210.3016-0.0001-0.48780.1257-0.6520.6449-0.20720.13970.3492-0.07880.946440.955116.773314.3037
301.23130.8026-0.55111.76830.2391.33630.2469-0.9573-0.4273-0.04630.0745-0.7448-0.1680.7588-0.49840.2949-0.15730.02120.5323-0.14440.548838.116312.381126.3635
310.25130.6912-0.8853.2769-1.32573.08090.16730.205-0.23110.56180.1669-0.3676-0.46040.1349-0.22520.23540.1009-0.0210.2915-0.09250.2422.92737.374755.4328
321.4905-2.0520.38542.1939-0.1792.34180.29780.29880.1446-0.0015-0.1664-0.3557-0.29160.1252-0.14150.32070.040.02220.3597-0.09290.3754-0.93458.819547.886
333.7855-1.5287-0.11051.93190.79870.4980.81271.1871-0.2945-0.4536-0.6886-0.14360.0901-0.3461-0.12580.3160.2814-0.06870.374-0.03710.221-9.3499.057239.7251
340.6162-0.7031.04085.129-1.52241.7488-0.4478-0.86010.2315-0.36040.0061-0.0596-0.73070.0860.17631.0930.40370.640.61070.29510.547-3.135122.501635.9327
350.66120.1335-0.46361.27150.85660.9626-0.11141.51170.2151-1.32640.6062-0.464-1.4135-0.081-0.28060.51550.7660.17810.00250.31840.2211-19.827426.99547.8435
362.41120.5208-0.78070.134-0.47733.9350.3888-0.03790.97260.08110.1280.3339-0.9661-0.1143-0.75330.59830.17750.20840.30450.11420.3885-13.154225.453948.0714
377.41883.4914-0.72612.9828-1.21757.3208-0.402-0.24910.7368-0.89480.0276-0.2738-1.10660.57560.18771.33260.57140.29780.34150.2540.5215-19.463335.032849.094
380.67230.3438-0.79440.330.02360.930.2490.17490.1939-0.796-0.08450.1839-0.6015-0.7386-0.07660.96230.73360.04450.73840.14880.2482-30.312432.082949.8074
393.2107-2.5382-1.54872.8582.39112.61540.58780.6885-0.2339-0.2417-0.7178-0.0923-0.8597-0.81630.0830.36830.35920.04810.52480.02620.348-22.285118.845545.5972
401.7151-1.23561.645.89020.61912.2916-0.2679-0.2889-0.2477-0.9137-0.51710.4651-0.3074-0.72750.28330.5010.4283-0.10070.8298-0.01060.4572-29.22519.057143.4276
411.65391.21150.30132.4720.09130.13810.7635-0.8017-0.22890.7527-0.5664-0.03570.296-0.8707-0.17570.428-0.2081-0.08430.58350.04660.226324.021756.648411.5059
420.89310.27570.86921.37870.72161.40730.6488-0.3722-0.2910.8446-0.0376-0.13510.3603-0.4994-0.24750.6586-0.233-0.15790.51760.1410.342727.132550.474511.0795
430.91990.9029-0.30721.6541.06021.42070.5009-0.1825-0.05360.6021-0.3155-0.2340.5545-0.8226-0.19410.4921-0.1468-0.11410.4343-0.0120.254725.403251.69341.5832
443.4281-0.72941.09060.72311.29523.66011.7070.6436-1.36560.4988-0.12190.80912.29020.1028-1.31981.37910.0318-0.72950.2555-0.16120.729132.697840.15481.8683
451.645-0.0808-1.11640.69510.44561.83560.6216-0.0864-1.58430.4346-0.10830.77871.58530.0239-0.73851.35550.0795-0.78320.3384-0.08621.241145.712234.729916.4504
462.5463-1.1053-0.7990.55510.2080.3862-0.71770.029-1.4721-0.03470.66930.51550.6036-0.3465-0.42651.2755-0.048-0.7820.32180.1671.077540.954536.331619.6129
471.84842.6877-4.24973.8407-6.16572.0104-2.1944-1.0742-1.01510.497-0.5923-0.09311.4524-0.16752.27761.25240.2320.02360.38980.05180.993550.717831.383421.7175
484.1759-0.3918-1.35050.0857-0.34773.8717-0.08620.1336-1.0233-0.0046-0.78490.03210.31391.05790.36931.36780.2731-0.69780.4905-0.13150.989758.885534.722923.6852
490.32050.2198-0.72870.0647-0.51411.76690.6002-0.1564-1.06970.6809-0.39110.25410.8695-0.4202-0.17280.82480.3518-0.46560.2589-0.28880.686548.492739.915310.6015
506.19760.0903-3.19286.6954-1.44011.92690.0533-0.54980.2799-1.4389-0.50760.15970.53840.2370.4251.21510.7619-0.34441.0504-0.28311.031854.627839.17388.0646
510.1809-0.42140.04041.2980.32980.70160.0582-0.54530.1886-0.0431-0.0879-0.05520.10580.0526-0.00430.2451-0.02060.15560.547-0.03530.28864.8413-5.40669.8527
523.7343-2.0396-0.99411.7167-0.07230.812-0.77850.61510.42670.33350.6205-0.33430.17541.1111-0.07340.2788-0.09590.0920.5887-0.3070.544513.3467-1.94038.6897
532.56870.26810.38670.112-0.19011.46270.0013-0.49350.66120.1715-0.10370.23950.26460.1610.10.2245-0.08040.00550.4006-0.12820.316-0.33550.4794.786
541.0486-0.1146-0.57990.98670.01710.5708-0.0248-0.21540.183-0.25490.1199-0.11130.1185-0.1019-0.02970.2646-0.06320.10560.3098-0.10340.21773.9336-5.11390.6927
558.64511.23523.71563.07560.85581.55960.2540.7863-0.8168-0.3076-0.3750.203-0.3220.00660.04450.2701-0.04620.12610.2143-0.00350.11731.9132-8.0339-6.8801
561.5291-0.5-0.33091.8572-0.79761.97730.64910.5780.377-0.0386-0.2245-0.02520.20390.0393-0.14670.38720.00020.10210.3270.01990.3218-0.86763.1789-9.1516
570.9245-0.38670.58031.048-0.82820.6159-0.0007-0.11530.6268-0.20420.01330.10450.44430.2874-0.07060.3722-0.05410.06230.29470.06660.3356-16.117210.7856-1.9287
583.1583-0.86980.06492.1013-0.73020.1493-0.2715-0.52050.62920.04440.4734-0.5883-0.2186-0.54-0.42950.1851-0.12330.09510.29040.01640.3737-13.840812.64380.045
591.15731.10780.00472.0197-0.78193.69810.0960.03820.221-0.07240.18110.30370.1629-0.5996-0.14170.1628-0.1621-0.04220.22910.12290.3905-24.18817.919-3.9175
601.76782.4822-0.79333.68580.05858.8601-0.47090.0377-1.8917-0.0856-0.3442-0.01780.1113-0.26221.14080.4461-0.1449-0.35480.19420.14360.631-28.08760.3497-4.4444
610.2051-0.53250.19931.0999-0.20460.62540.3394-0.6468-0.1588-0.285-0.35210.510.1266-0.1783-0.09670.2567-0.0029-0.130.4335-0.06160.429720.466370.60766.8135
620.2971-0.00320.40020.2850.09360.3323-0.11660.1670.17280.26450.02490.1075-0.5755-1.17710.05570.31340.1138-0.07590.62960.06230.353813.368469.0667.6984
632.2424-1.08831.25341.2688-0.38051.7674-0.0009-0.29290.03-0.1065-0.0864-0.086-0.0695-0.25150.08130.26310.0468-0.05810.2420.01360.215625.613265.529461.7969
643.0181-1.92550.76532.01060.16920.64951.06110.27050.2632-1.4228-0.647-0.0619-0.7298-0.2779-0.03870.48110.0824-0.15020.1851-0.05630.237719.058666.473453.3159
650.6852-0.70860.70320.9806-0.03442.7582-0.00390.2857-0.9082-0.34690.3665-0.48571.1013-0.3258-0.39430.5637-0.0349-0.10640.30070.06540.533926.344152.98256.7873
661.465-0.56020.21120.6065-0.87791.7681-0.19-0.3603-0.5462-0.6179-0.16640.07310.4238-0.23990.33780.3870.04440.01710.1760.09530.589642.254548.929765.1882
671.5198-0.1858-0.09020.0574-0.00771.3357-0.1896-0.2289-0.2865-0.03380.1745-0.15170.191-0.1520.03260.31550.05630.0330.25180.15180.528141.477754.047570.5611
680.05950.01180.00882.4095-1.34730.74570.1816-0.0421-0.13270.3197-0.4137-0.71550.0173-0.03410.39560.20050.09420.06940.23530.23420.665253.24351.118370.5755
690.61460.335-0.87193.17981.15872.3718-0.3618-0.1777-0.4959-0.38050.2349-0.5206-0.12840.17420.05240.16190.0490.19820.08730.1320.454550.275954.323262.6558
701.2623-1.0436-1.73074.7546-0.50673.09510.9713-0.18051.0882-2.0578-0.86250.4144-0.06971.02890.10980.0432-0.70390.7264-1.38730.9076-0.054248.109255.740255.7998
710.47310.1751-0.39931.05310.65450.9422-0.16820.1127-0.13240.31410.590.0902-0.16990.279-0.45020.2828-0.0534-0.08550.7149-0.02380.361515.674440.2758-21.6937
722.0214-0.0672-1.72124.0276-0.0521.6954-1.99990.6848-0.86060.22041.1956-0.49970.7411-0.5216-0.3686-0.4042-0.3866-0.54220.6397-0.3067-0.060523.899842.9548-23.059
731.09870.46270.0761.599-0.98541.69940.15650.2266-0.23310.1171-0.0460.4536-0.06610.1896-0.06610.1641-0.09180.00640.4533-0.06080.312810.278738.8432-16.2786
744.69531.3863-0.99381.5329-1.05760.89420.62420.0357-0.27910.5577-0.0552-0.167-0.33890.2387-0.28750.3531-0.15430.03110.3866-0.11440.194221.709445.9104-10.8079
752.21370.0838-0.10832.9820.4732.20830.5828-0.6348-0.22360.53340.0351-0.1082-0.10630.3212-0.29610.611-0.09990.02960.6857-0.04350.53079.377933.6521-4.8646
760.1325-0.1399-0.37950.9272-0.1521.00260.05670.0797-0.66320.160.06430.5744-0.2303-0.3321-0.06010.1779-0.07390.01180.33430.24380.5272-7.47628.4763-13.517
771.2961.027-2.01691.0098-1.82534.14320.0443-0.5166-0.251-0.31610.11510.23920.20140.4036-0.0090.1449-0.0167-0.02070.35670.15540.5143-2.178827.0563-14.2706
783.8391-0.0347-0.98051.6505-0.03380.1906-0.4276-1.51132.54870.0892-0.12361.1784-0.8884-1.3062-0.3408-0.0359-0.23080.11970.54470.57530.3727-16.164224.8895-16.6266
791.46561.1279-0.63421.8452-0.9941.33890.77691.00810.86910.33690.25191.23060.0505-0.4501-0.84950.33120.03760.17560.62320.22210.7732-13.056633.3382-10.8241
800.82440.1381-0.50721.3093-0.10740.81410.8639-0.60720.13040.16360.17590.3503-0.4647-0.8282-0.86810.44060.1470.21750.8910.20160.8206-12.023137.053-6.3272
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 646:665)A646 - 665
2X-RAY DIFFRACTION2(CHAIN A AND RESID 666:690)A666 - 690
3X-RAY DIFFRACTION3(CHAIN A AND RESID 691:734)A691 - 734
4X-RAY DIFFRACTION4(CHAIN A AND RESID 735:751)A735 - 751
5X-RAY DIFFRACTION5(CHAIN A AND RESID 752:763)A752 - 763
6X-RAY DIFFRACTION6(CHAIN A AND RESID 764:773)A764 - 773
7X-RAY DIFFRACTION7(CHAIN A AND RESID 774:784)A774 - 784
8X-RAY DIFFRACTION8(CHAIN A AND RESID 785:802)A785 - 802
9X-RAY DIFFRACTION9(CHAIN A AND RESID 803:824)A803 - 824
10X-RAY DIFFRACTION10(CHAIN A AND RESID 825:834)A825 - 834
11X-RAY DIFFRACTION11(CHAIN B AND RESID 646:660)B646 - 660
12X-RAY DIFFRACTION12(CHAIN B AND RESID 661:685)B661 - 685
13X-RAY DIFFRACTION13(CHAIN B AND RESID 686:732)B686 - 732
14X-RAY DIFFRACTION14(CHAIN B AND RESID 733:752)B733 - 752
15X-RAY DIFFRACTION15(CHAIN B AND RESID 753:763)B753 - 763
16X-RAY DIFFRACTION16(CHAIN B AND RESID 764:773)B764 - 773
17X-RAY DIFFRACTION17(CHAIN B AND RESID 774:784)B774 - 784
18X-RAY DIFFRACTION18(CHAIN B AND RESID 785:796)B785 - 796
19X-RAY DIFFRACTION19(CHAIN B AND RESID 797:803)B797 - 803
20X-RAY DIFFRACTION20(CHAIN B AND RESID 804:834)B804 - 834
21X-RAY DIFFRACTION21(CHAIN C AND RESID 644:657)C644 - 657
22X-RAY DIFFRACTION22(CHAIN C AND RESID 658:673)C658 - 673
23X-RAY DIFFRACTION23(CHAIN C AND RESID 674:681)C674 - 681
24X-RAY DIFFRACTION24(CHAIN C AND RESID 682:721)C682 - 721
25X-RAY DIFFRACTION25(CHAIN C AND RESID 722:734)C722 - 734
26X-RAY DIFFRACTION26(CHAIN C AND RESID 735:751)C735 - 751
27X-RAY DIFFRACTION27(CHAIN C AND RESID 752:762)C752 - 762
28X-RAY DIFFRACTION28(CHAIN C AND RESID 763:783)C763 - 783
29X-RAY DIFFRACTION29(CHAIN C AND RESID 784:803)C784 - 803
30X-RAY DIFFRACTION30(CHAIN C AND RESID 804:834)C804 - 834
31X-RAY DIFFRACTION31(CHAIN D AND RESID 646:669)D646 - 669
32X-RAY DIFFRACTION32(CHAIN D AND RESID 670:727)D670 - 727
33X-RAY DIFFRACTION33(CHAIN D AND RESID 728:743)D728 - 743
34X-RAY DIFFRACTION34(CHAIN D AND RESID 744:753)D744 - 753
35X-RAY DIFFRACTION35(CHAIN D AND RESID 754:773)D754 - 773
36X-RAY DIFFRACTION36(CHAIN D AND RESID 774:783)D774 - 783
37X-RAY DIFFRACTION37(CHAIN D AND RESID 784:790)D784 - 790
38X-RAY DIFFRACTION38(CHAIN D AND RESID 791:809)D791 - 809
39X-RAY DIFFRACTION39(CHAIN D AND RESID 810:823)D810 - 823
40X-RAY DIFFRACTION40(CHAIN D AND RESID 824:834)D824 - 834
41X-RAY DIFFRACTION41(CHAIN E AND RESID 646:667)E646 - 667
42X-RAY DIFFRACTION42(CHAIN E AND RESID 668:697)E668 - 697
43X-RAY DIFFRACTION43(CHAIN E AND RESID 698:728)E698 - 728
44X-RAY DIFFRACTION44(CHAIN E AND RESID 729:753)E729 - 753
45X-RAY DIFFRACTION45(CHAIN E AND RESID 754:769)E754 - 769
46X-RAY DIFFRACTION46(CHAIN E AND RESID 770:790)E770 - 790
47X-RAY DIFFRACTION47(CHAIN E AND RESID 791:798)E791 - 798
48X-RAY DIFFRACTION48(CHAIN E AND RESID 799:807)E799 - 807
49X-RAY DIFFRACTION49(CHAIN E AND RESID 808:824)E808 - 824
50X-RAY DIFFRACTION50(CHAIN E AND RESID 825:834)E825 - 834
51X-RAY DIFFRACTION51(CHAIN F AND RESID 646:666)F646 - 666
52X-RAY DIFFRACTION52(CHAIN F AND RESID 667:675)F667 - 675
53X-RAY DIFFRACTION53(CHAIN F AND RESID 676:692)F676 - 692
54X-RAY DIFFRACTION54(CHAIN F AND RESID 693:723)F693 - 723
55X-RAY DIFFRACTION55(CHAIN F AND RESID 724:732)F724 - 732
56X-RAY DIFFRACTION56(CHAIN F AND RESID 733:750)F733 - 750
57X-RAY DIFFRACTION57(CHAIN F AND RESID 751:773)F751 - 773
58X-RAY DIFFRACTION58(CHAIN F AND RESID 774:788)F774 - 788
59X-RAY DIFFRACTION59(CHAIN F AND RESID 789:829)F789 - 829
60X-RAY DIFFRACTION60(CHAIN F AND RESID 830:834)F830 - 834
61X-RAY DIFFRACTION61(CHAIN G AND RESID 644:666)G644 - 666
62X-RAY DIFFRACTION62(CHAIN G AND RESID 667:676)G667 - 676
63X-RAY DIFFRACTION63(CHAIN G AND RESID 677:717)G677 - 717
64X-RAY DIFFRACTION64(CHAIN G AND RESID 718:733)G718 - 733
65X-RAY DIFFRACTION65(CHAIN G AND RESID 734:751)G734 - 751
66X-RAY DIFFRACTION66(CHAIN G AND RESID 752:766)G752 - 766
67X-RAY DIFFRACTION67(CHAIN G AND RESID 767:790)G767 - 790
68X-RAY DIFFRACTION68(CHAIN G AND RESID 791:802)G791 - 802
69X-RAY DIFFRACTION69(CHAIN G AND RESID 803:821)G803 - 821
70X-RAY DIFFRACTION70(CHAIN G AND RESID 822:834)G822 - 834
71X-RAY DIFFRACTION71(CHAIN H AND RESID 645:659)H645 - 659
72X-RAY DIFFRACTION72(CHAIN H AND RESID 660:673)H660 - 673
73X-RAY DIFFRACTION73(CHAIN H AND RESID 674:711)H674 - 711
74X-RAY DIFFRACTION74(CHAIN H AND RESID 712:731)H712 - 731
75X-RAY DIFFRACTION75(CHAIN H AND RESID 732:752)H732 - 752
76X-RAY DIFFRACTION76(CHAIN H AND RESID 753:773)H753 - 773
77X-RAY DIFFRACTION77(CHAIN H AND RESID 774:786)H774 - 786
78X-RAY DIFFRACTION78(CHAIN H AND RESID 787:802)H787 - 802
79X-RAY DIFFRACTION79(CHAIN H AND RESID 803:822)H803 - 822
80X-RAY DIFFRACTION80(CHAIN H AND RESID 823:834)H823 - 834

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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

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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

+
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。

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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