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- PDB-6wg6: Crystal structure of human SMC1-SMC3 hinge domain heterodimer in ... -

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基本情報

登録情報
データベース: PDB / ID: 6wg6
タイトルCrystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation
要素
  • Structural maintenance of chromosomes protein
  • Structural maintenance of chromosomes protein 3
  • poly(dT)
キーワードCELL CYCLE/DNA / Protein-DNA complex / ATPase / DNA-binding protein / Genome organization / Sister chromatid cohesion / Transcription regulation / CELL CYCLE / CELL CYCLE-DNA complex
機能・相同性
機能・相同性情報


response to DNA damage checkpoint signaling / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / lateral element / mediator complex binding / establishment of mitotic sister chromatid cohesion ...response to DNA damage checkpoint signaling / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / lateral element / mediator complex binding / establishment of mitotic sister chromatid cohesion / microtubule motor activity / sister chromatid cohesion / mitotic sister chromatid cohesion / stem cell population maintenance / mitotic spindle pole / dynein complex binding / beta-tubulin binding / regulation of DNA replication / mitotic sister chromatid segregation / somatic stem cell population maintenance / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / cis-regulatory region sequence-specific DNA binding / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / response to radiation / kinetochore / nuclear matrix / Separation of Sister Chromatids / mitotic cell cycle / chromosome / double-stranded DNA binding / Estrogen-dependent gene expression / protein heterodimerization activity / cell division / DNA repair / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol
類似検索 - 分子機能
Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Smc1, ATP-binding cassette domain / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
DNA / Structural maintenance of chromosomes protein / Structural maintenance of chromosomes protein 1A / Structural maintenance of chromosomes protein 3
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: 3.54 Å
データ登録者Shi, Z.B. / Yu, H.
資金援助 米国, 2件
組織認可番号国
Cancer Prevention and Research Institute of Texas (CPRIT) 米国
Welch Foundation 米国
引用ジャーナル: Science / 年: 2020
タイトル: Cryo-EM structure of the human cohesin-NIPBL-DNA complex.
著者: Zhubing Shi / Haishan Gao / Xiao-Chen Bai / Hongtao Yu /
要旨: As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How ...As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo-electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72-base pair DNA. NIPBL and DNA promote the engagement of cohesin's ATPase head domains and ATP binding. The hinge domains of cohesin adopt an "open washer" conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.
履歴
登録2020年4月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年5月20日Provider: repository / タイプ: Initial release
改定 1.12020年5月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22020年7月8日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32022年10月26日Group: Database references / Derived calculations
カテゴリ: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Structural maintenance of chromosomes protein
B: Structural maintenance of chromosomes protein 3
C: Structural maintenance of chromosomes protein
D: Structural maintenance of chromosomes protein 3
E: Structural maintenance of chromosomes protein
F: Structural maintenance of chromosomes protein 3
G: Structural maintenance of chromosomes protein
H: Structural maintenance of chromosomes protein 3
I: Structural maintenance of chromosomes protein
J: Structural maintenance of chromosomes protein 3
K: Structural maintenance of chromosomes protein
L: Structural maintenance of chromosomes protein 3
M: poly(dT)
N: poly(dT)


分子量 (理論値)分子数
合計 (水以外)342,79314
ポリマ－342,79314
非ポリマー00
水00
1
A: Structural maintenance of chromosomes protein
B: Structural maintenance of chromosomes protein 3
M: poly(dT)


分子量 (理論値)分子数
合計 (水以外)59,1303
ポリマ－59,1303
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Structural maintenance of chromosomes protein
D: Structural maintenance of chromosomes protein 3
N: poly(dT)


分子量 (理論値)分子数
合計 (水以外)59,1303
ポリマ－59,1303
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Structural maintenance of chromosomes protein
F: Structural maintenance of chromosomes protein 3


分子量 (理論値)分子数
合計 (水以外)56,1332
ポリマ－56,1332
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Structural maintenance of chromosomes protein
H: Structural maintenance of chromosomes protein 3


分子量 (理論値)分子数
合計 (水以外)56,1332
ポリマ－56,1332
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Structural maintenance of chromosomes protein
J: Structural maintenance of chromosomes protein 3


分子量 (理論値)分子数
合計 (水以外)56,1332
ポリマ－56,1332
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Structural maintenance of chromosomes protein
L: Structural maintenance of chromosomes protein 3


分子量 (理論値)分子数
合計 (水以外)56,1332
ポリマ－56,1332
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)123.985, 145.021, 315.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

#1: タンパク質
Structural maintenance of chromosomes protein


分子量: 26710.809 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SMC1A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: G8JLG1, UniProt: Q14683*PLUS
#2: タンパク質
Structural maintenance of chromosomes protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate ...SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate proteoglycan 6 / Chromosome-associated polypeptide / hCAP


分子量: 29422.336 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SMC3, BAM, BMH, CSPG6, SMC3L1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UQE7
#3: DNA鎖 poly(dT)


分子量: 2996.971 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)

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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: 4.14 Å3/Da / 溶媒含有率: 70.31 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 4
詳細: 0.1 M sodium acetate pH 4.0, 15% polyethylene glycol 400

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
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: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年10月12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: 0.9792 Å / 相対比: 1
反射解像度: 3.54→50 Å / Num. obs: 61430 / % possible obs: 100 % / 冗長度: 12.8 % / Biso Wilson estimate: 51.35 Å2 / CC1/2: 0.974 / CC star: 0.993 / Net I/σ(I): 5
反射 シェル解像度: 3.54→3.61 Å / 冗長度: 13 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2413 / CC1/2: 0.177 / CC star: 0.548 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
HKL-3000データ削減
HKL-3000データスケーリング
PHENIX位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 2WD5

2wd5


解像度: 3.54→49.5 Å / SU ML: 0.4375 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.2457
Rfactor反射数%反射
Rfree0.2883 1982 3.25 %
Rwork0.2518 --
obs0.253 60986 87.26 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 79.61 Å2
精密化ステップサイクル: LAST / 解像度: 3.54→49.5 Å
タンパク質核酸リガンド溶媒全体
原子数19958 80 0 0 20038
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003720356
X-RAY DIFFRACTIONf_angle_d0.741927371
X-RAY DIFFRACTIONf_chiral_restr0.04563002
X-RAY DIFFRACTIONf_plane_restr0.00533565
X-RAY DIFFRACTIONf_dihedral_angle_d22.76462783
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.54-3.630.4863430.32461284X-RAY DIFFRACTION27.11
3.63-3.730.3521010.31262972X-RAY DIFFRACTION62.38
3.73-3.840.32851220.29713642X-RAY DIFFRACTION76.66
3.84-3.970.2981350.29414007X-RAY DIFFRACTION83.93
3.97-4.110.35111420.28114254X-RAY DIFFRACTION88.65
4.11-4.270.29251550.27054589X-RAY DIFFRACTION95.82
4.27-4.470.26161580.25724711X-RAY DIFFRACTION98.62
4.47-4.70.27261610.234763X-RAY DIFFRACTION99.27
4.7-50.2861610.23344777X-RAY DIFFRACTION98.88
5-5.380.3121610.24784769X-RAY DIFFRACTION99.02
5.38-5.920.32111600.27764793X-RAY DIFFRACTION99
5.92-6.780.33091640.26744860X-RAY DIFFRACTION99.68
6.78-8.530.22731660.22524917X-RAY DIFFRACTION99.73
8.53-49.50.22221530.18544666X-RAY DIFFRACTION91.06
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)
10.2021313842880.341768414464-0.1443023525730.576603869665-0.2438374963810.1025948960730.1487024050850.05524603079580.118832789681-0.633118057526-0.7558172303460.170448447235-0.658872992361-0.8648748723120.3458049438962.524767937180.855779731920.2000431323861.70152783445-0.1638636754941.0204741058-8.78164670953-5.5733853202928.6114487059
21.915054992630.2324958150230.08983488123741.052258688240.2013503389091.78452109214-0.537607941915-0.4236660129110.357997775667-0.1321466332020.1153238074870.541604073045-0.48480371951-1.33568938550.3805263945731.169467448270.436709412087-0.1287385655932.12807835766-0.2728195546610.607237465978-10.1686113883-15.945032950121.6593184837
31.084643437210.2109616513270.6370129595072.14181111505-0.874748880511.8303074448-0.3385176638750.7434281677090.07664795728150.7161321228480.4464691534690.3691955385340.352795799507-1.25913509593-0.1166933661931.142020988130.01960572242050.08487357435082.25053571368-0.1154349319390.949512244094-10.8360617565-31.104176633120.0189030289
46.591748950072.79061491694.285019946492.785148069682.608453669434.929792940520.421520164182-0.5557007787020.32373666355-0.128767839379-0.9169418645820.0274032626457-0.367931822811-0.6057011721650.5233649075490.712555977804-0.000659738443218-0.2932005724120.6366656356220.02235378980280.62714120462433.1238589247-6.0530147404943.7639078504
51.46461747976-0.470768594459-0.0792934483751.99409577166-0.9663877860563.17230070157-0.3643795044380.3712582085320.197445773662-0.300090198239-0.1621670725030.236178545067-0.2260218261790.05482902596360.2727444080680.6435011862950.0246934783195-0.3223157361790.86478802466-0.004708783201610.20920995203915.7743026546-25.767602749619.5281049543
62.280466634370.08051904178610.2317851043172.43722319593-0.4717866352142.721308743350.1603213512220.757855748046-0.120008738915-0.760044611207-0.114893299999-0.727587572407-0.4609828695630.7504271072770.02697769026420.735540508867-0.183451828996-0.003348478636230.894754363449-0.1763301131630.91802779812137.8499592178-9.5366169305935.3073835689
77.210900840011.94043374544-3.608708635979.19524282929-1.545555819267.001148992150.16908336589-0.4776986459930.2272653985380.2965568103180.441044893889-0.302421580863-0.2158851127010.788293670488-0.512258448711.05276581209-0.215041359211-0.1578487638431.16207159559-0.01205767367481.07401961419-14.7825856418-17.677325951798.336184051
84.465820852965.58187532313-2.779926352018.67254522166-1.793936210845.490312838110.21541026956-1.431246716470.133106137460.925522558232-0.4502359276160.7578807140340.13101018893-0.7516007378840.1401910366621.311933139310.05207597997410.1847647987661.379294255730.2896356489850.974722202444-47.664802163-50.331276561198.5304653388
92.041112333590.385932009204-0.01556977215492.050688451110.2342398110352.838040860790.201484245519-0.1253343188841.02873951641-0.412891517062-0.0996038840796-0.288648402622-1.243912460030.0151011150131-0.1633875953630.7472067762340.03119880250350.1090736644320.195678060567-0.07147054653230.692127941663-16.6601128491-16.608829167267.7732443974
101.2364203882-0.6326418613710.5885191798310.505508344378-0.8623115123732.06196054856-0.434749314453-0.5965034209810.8577333213170.10079818032-0.0149038299686-0.405199798941-0.8227568062190.01078465287110.2472001166830.3976901821510.0103959622086-0.1296702159690.332944336578-0.2782756164551.04069603776-8.09010880138-18.13785143183.2795843887
112.7194520459-1.116215843091.342452518372.074799415790.5371131118326.47494030.118915759135-0.364263487155-0.110076441713-0.006964693252920.175810527744-0.01811276717380.422711577111-0.05791592001530.1419569453210.1344296469760.1093340807190.155073165860.0541235204995-0.08104697188550.532578018113-16.5965273471-28.312013995980.4038452506
121.33051877581-0.619594648774-1.586114835452.43500736750.4579101190731.93746702714-0.41367627687-0.809301910950.80494128670.8494677296470.474893457534-0.921997460623-0.14643995520.521555695934-0.1233233246750.5866463727150.228946910377-0.2556155897020.313485522973-0.2964640637450.768220728729-6.65612093384-22.078952783793.4513665594
133.08412574209-1.130653156860.2276275753363.22508126652-0.2193328723711.97611265084-0.1195794817670.150007831782-0.1236413958290.09269475385130.401437958516-0.593669460854-0.06266069028570.834650999897-0.3378571490950.5130493656380.0438210557482-0.06004087888030.776456508741-0.2535360716271.175455916863.86786954504-21.750149113987.0996564171
140.907807930047-0.5334590571-1.609054037581.038490488710.5412508467345.17027854909-0.1161056698970.614344961366-0.110131774299-0.3781864273080.01673704572680.193729760558-0.377603039633-0.183345778797-0.1298648431590.3363260899-0.1822481769270.2057296247850.725447177529-0.1735446097160.648450090186.80330935486-36.872920739336.4906691647
152.318446284530.544481000490.1608254008270.7703383879120.4009874274941.046772242810.0123178461768-0.0323727813649-0.6057035748320.1134369200270.00140200475915-0.5135954644970.1450889106830.221165345186-0.0512099122150.0904074208776-0.177033039080.1333125561270.110455407173-0.184684439160.96272308506110.0401964833-43.444804346169.1123367936
161.36918947292-0.4642530986250.1153393945072.355522446360.642847453171.397962355320.08051379715530.120369480667-0.526978256101-0.171096552397-0.1678318181980.1967504589550.0706293412185-0.302303702430.2354381742350.209856548218-0.01780574607730.1267212223230.215473082026-0.3239972505040.60072369874-10.2574380465-43.138416999171.571088169
171.13134285982-1.6456027479-0.4650906866322.808265231760.4613162628511.356602922220.09149916620530.450349931405-0.137820945346-0.561859060246-0.3024144524610.1004284931830.652040451495-0.3423392970520.1844626541720.765434316513-0.1755648008580.3416172295940.581019862195-0.1393453043340.6874593158196.30593843328-46.454885497340.7882739506
180.9161708040170.3936168976930.7500421810881.73133217935-0.4580268021661.259700731870.09364729589350.0927034026571-0.176177351126-1.04099930921-0.1568886363860.1907720851860.311754651445-0.141095696484-0.02649813054660.686300226256-0.1056157765420.1076249894630.343901033104-0.3805699787851.11960986108-45.1739630878-51.059131382967.8011378122
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661.81605842921.42001083589-0.2094701955713.495363933892.784298557173.72128818530.423959652034-0.1133029354080.03282338312320.2094587927970.359324905216-0.638416086541-0.1627716862580.73352383148-0.5872527590271.8740356873-0.32186373481-0.3349652834091.021924945930.04876802160191.0231843469-52.0110123061-41.163789757233.9071438172
672.34494299376-0.778054486425-1.629355233251.003407378090.4766488819712.63852676815-0.121625873512-0.110211029089-0.1587649915310.2814586707430.2364748586040.08466674914340.2783883194470.2002782472032.33364711550.597858534978-0.03634960416780.3441318500740.300761581545-0.3660811405370.436113914917-93.6750400966-61.051546890743.1628080942
681.41798913752-1.10642388947-0.51180668242.089350743511.144832114360.724317603311-0.196852141915-0.0613120224433-0.0484563531138-0.0226494122393-0.2679942891210.568395713266-0.420123103341-0.5225183418390.1408560073220.5816404222720.1283463941390.03790068964170.770509188718-0.4750525673580.448352376658-86.9331235998-35.262831890430.6681322439
692.50993308237-0.211605592977-0.1557209128571.507830834450.3200302265462.24346233678-0.5806597530710.04235059574730.0792380989219-0.262622006644-0.2863145834370.468657403819-0.518343284835-0.207664751299-0.2792250777290.6225625578680.120868175722-0.1118621681310.550151347366-0.2975719578920.33604125436-79.5113755408-36.969771060225.2719397885
704.10622855403-1.533673886881.840110827898.144620300221.838780367155.859078251070.2292819257120.3092820588390.146075909081-1.22775320953-0.3497040817820.394385172199-0.2530769823750.1442930171420.3200724392510.3175907836950.174199426663-0.1882195494560.340992123413-0.296171085820.730232223165-78.2989521098-31.463214096427.051303838
711.30122038783-1.76533438978-0.2778154850938.432155789985.591877840764.82531995891-0.1465987781480.254910924679-0.130264061121-0.324602248407-0.7581801929730.838754355771-0.706962659679-0.03635201703940.837614977491.02660672386-0.2074456119070.02949183028281.23785515041-0.2970794043291.14534547816-76.1837126503-43.30562269172.79298950587
722.16845597335-0.1962032334320.6117175783792.755212846380.552322615761.66498833631-0.5521227229940.107556681507-0.252726583613-0.446268709634-0.1897019544290.05001999857710.2358975526440.1029654854510.217321228560.531647965915-0.006373568305740.2800346550140.763160819651-0.188358912030.251466375631-72.967654196-49.993480724811.8763006145
731.675155815730.467972553428-1.751529691541.37581224468-0.8875360204463.88917306433-0.04449507969590.720195618891-0.1330879520710.04301021213040.2998578032780.147756121950.0610282415806-1.063678945610.2749971678580.792777201343-0.2041415293120.1989505838360.892630973365-0.1411770580360.2218923389-99.6775550433-58.398789254635.3377950533
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'K' and (resid 496 through 510 )
2X-RAY DIFFRACTION2chain 'K' and (resid 511 through 563 )
3X-RAY DIFFRACTION3chain 'K' and (resid 564 through 670 )
4X-RAY DIFFRACTION4chain 'L' and (resid 468 through 499 )
5X-RAY DIFFRACTION5chain 'L' and (resid 500 through 673 )
6X-RAY DIFFRACTION6chain 'L' and (resid 674 through 706 )
7X-RAY DIFFRACTION7chain 'M' and (resid 9 through 10 )
8X-RAY DIFFRACTION8chain 'N' and (resid 3 through 4 )
9X-RAY DIFFRACTION9chain 'A' and (resid 495 through 510 )
10X-RAY DIFFRACTION10chain 'A' and (resid 511 through 543 )
11X-RAY DIFFRACTION11chain 'A' and (resid 544 through 587 )
12X-RAY DIFFRACTION12chain 'A' and (resid 588 through 621 )
13X-RAY DIFFRACTION13chain 'A' and (resid 622 through 676 )
14X-RAY DIFFRACTION14chain 'B' and (resid 469 through 500 )
15X-RAY DIFFRACTION15chain 'B' and (resid 501 through 604 )
16X-RAY DIFFRACTION16chain 'B' and (resid 605 through 673 )
17X-RAY DIFFRACTION17chain 'B' and (resid 674 through 704 )
18X-RAY DIFFRACTION18chain 'C' and (resid 495 through 510 )
19X-RAY DIFFRACTION19chain 'C' and (resid 511 through 527 )
20X-RAY DIFFRACTION20chain 'C' and (resid 528 through 563 )
21X-RAY DIFFRACTION21chain 'C' and (resid 564 through 573 )
22X-RAY DIFFRACTION22chain 'C' and (resid 574 through 586 )
23X-RAY DIFFRACTION23chain 'C' and (resid 587 through 602 )
24X-RAY DIFFRACTION24chain 'C' and (resid 603 through 630 )
25X-RAY DIFFRACTION25chain 'C' and (resid 631 through 645 )
26X-RAY DIFFRACTION26chain 'C' and (resid 646 through 658 )
27X-RAY DIFFRACTION27chain 'C' and (resid 659 through 676 )
28X-RAY DIFFRACTION28chain 'D' and (resid 468 through 500 )
29X-RAY DIFFRACTION29chain 'D' and (resid 501 through 578 )
30X-RAY DIFFRACTION30chain 'D' and (resid 579 through 591 )
31X-RAY DIFFRACTION31chain 'D' and (resid 592 through 604 )
32X-RAY DIFFRACTION32chain 'D' and (resid 605 through 626 )
33X-RAY DIFFRACTION33chain 'D' and (resid 627 through 673 )
34X-RAY DIFFRACTION34chain 'D' and (resid 674 through 702 )
35X-RAY DIFFRACTION35chain 'E' and (resid 494 through 510 )
36X-RAY DIFFRACTION36chain 'E' and (resid 511 through 547 )
37X-RAY DIFFRACTION37chain 'E' and (resid 548 through 562 )
38X-RAY DIFFRACTION38chain 'E' and (resid 563 through 582 )
39X-RAY DIFFRACTION39chain 'E' and (resid 583 through 594 )
40X-RAY DIFFRACTION40chain 'E' and (resid 595 through 630 )
41X-RAY DIFFRACTION41chain 'E' and (resid 631 through 655 )
42X-RAY DIFFRACTION42chain 'E' and (resid 656 through 671 )
43X-RAY DIFFRACTION43chain 'F' and (resid 469 through 500 )
44X-RAY DIFFRACTION44chain 'F' and (resid 501 through 577 )
45X-RAY DIFFRACTION45chain 'F' and (resid 578 through 591 )
46X-RAY DIFFRACTION46chain 'F' and (resid 592 through 661 )
47X-RAY DIFFRACTION47chain 'F' and (resid 662 through 703 )
48X-RAY DIFFRACTION48chain 'G' and (resid 494 through 510 )
49X-RAY DIFFRACTION49chain 'G' and (resid 511 through 586 )
50X-RAY DIFFRACTION50chain 'G' and (resid 587 through 671 )
51X-RAY DIFFRACTION51chain 'H' and (resid 469 through 500 )
52X-RAY DIFFRACTION52chain 'H' and (resid 501 through 577 )
53X-RAY DIFFRACTION53chain 'H' and (resid 578 through 591 )
54X-RAY DIFFRACTION54chain 'H' and (resid 592 through 634 )
55X-RAY DIFFRACTION55chain 'H' and (resid 635 through 673 )
56X-RAY DIFFRACTION56chain 'H' and (resid 674 through 704 )
57X-RAY DIFFRACTION57chain 'I' and (resid 496 through 510 )
58X-RAY DIFFRACTION58chain 'I' and (resid 511 through 528 )
59X-RAY DIFFRACTION59chain 'I' and (resid 529 through 543 )
60X-RAY DIFFRACTION60chain 'I' and (resid 544 through 572 )
61X-RAY DIFFRACTION61chain 'I' and (resid 573 through 591 )
62X-RAY DIFFRACTION62chain 'I' and (resid 592 through 605 )
63X-RAY DIFFRACTION63chain 'I' and (resid 606 through 630 )
64X-RAY DIFFRACTION64chain 'I' and (resid 631 through 640 )
65X-RAY DIFFRACTION65chain 'I' and (resid 641 through 656 )
66X-RAY DIFFRACTION66chain 'I' and (resid 657 through 668 )
67X-RAY DIFFRACTION67chain 'J' and (resid 469 through 500 )
68X-RAY DIFFRACTION68chain 'J' and (resid 501 through 542 )
69X-RAY DIFFRACTION69chain 'J' and (resid 543 through 578 )
70X-RAY DIFFRACTION70chain 'J' and (resid 579 through 591 )
71X-RAY DIFFRACTION71chain 'J' and (resid 592 through 604 )
72X-RAY DIFFRACTION72chain 'J' and (resid 605 through 673 )
73X-RAY DIFFRACTION73chain 'J' and (resid 674 through 706 )

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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