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- EMDB-11869: Structure of the actin filament Arp2/3 complex branch junction in... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-11869
タイトルStructure of the actin filament Arp2/3 complex branch junction in cells
マップデータStructure of the actin filament Arp2/3 complex branch junction
試料
  • 細胞: Actin Filament Arp2/3 Complex Branch Junction
    • タンパク質・ペプチド: Actin-related protein 2, Arp2
    • タンパク質・ペプチド: Actin-related protein 3, Arp3
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 1b, ArpC1b
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 2, ArpC2
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 3, ArpC3
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 4, ArpC4
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 5, ArpC5
    • タンパク質・ペプチド: Actin, alpha skeletal muscle, ACTA1アクチン
キーワードActin (アクチン) / Arp2-3 complex / Cytoskeleton (細胞骨格) / STRUCTURAL PROTEIN (タンパク質)
機能・相同性
機能・相同性情報


podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization ...podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / peripheral region of growth cone / : / meiotic cytokinesis / muscle cell projection membrane / apical ectoplasmic specialization / basal ectoplasmic specialization / cellular response to rapamycin / lamellipodium organization / spindle localization / skeletal muscle fiber adaptation / cellular response to trichostatin A / leading edge of lamellipodium / Striated Muscle Contraction / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / 半接着斑 / asymmetric cell division / protein kinase C signaling / Arp2/3 complex-mediated actin nucleation / actin filament network formation / podosome ring / orbitofrontal cortex development / actin cap / postsynaptic actin cytoskeleton organization / Regulation of actin dynamics for phagocytic cup formation / negative regulation of axon extension / positive regulation of dendritic spine morphogenesis / maintenance of cell polarity / Clathrin-mediated endocytosis / positive regulation of astrocyte differentiation / cellular response to organonitrogen compound / apical dendrite / : / astrocyte differentiation / podosome / positive regulation of fibroblast migration / positive regulation of synapse assembly / positive regulation of podosome assembly / response to steroid hormone / positive regulation of dendrite morphogenesis / positive regulation of filopodium assembly / smooth muscle cell migration / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cellular response to platelet-derived growth factor stimulus / mesenchyme migration / positive regulation of smooth muscle cell migration / cell leading edge / filamentous actin / 学習 / skeletal muscle thin filament assembly / 刷子縁 / striated muscle thin filament / excitatory synapse / cilium assembly / positive regulation of double-strand break repair via homologous recombination / response to immobilization stress / positive regulation of protein targeting to membrane / glutamate receptor binding / positive regulation of lamellipodium assembly / skeletal muscle fiber development / axon terminus / response to mechanical stimulus / positive regulation of substrate adhesion-dependent cell spreading / stress fiber / cellular response to epidermal growth factor stimulus / ruffle / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / actin filament polymerization / positive regulation of neuron differentiation / Neutrophil degranulation / cellular response to nerve growth factor stimulus / meiotic cell cycle / 分泌 / dendritic shaft / filopodium / cell projection / マイクロフィラメント / positive regulation of protein localization to plasma membrane / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / structural constituent of cytoskeleton / ruffle membrane / cellular response to type II interferon / actin filament binding / cell-cell junction
類似検索 - 分子機能
Actin-related protein 3 / Actin-related protein 2/3 complex subunit 1B / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily ...Actin-related protein 3 / Actin-related protein 2/3 complex subunit 1B / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 16 kDa subunit (p16-Arc) / ARP2/3 complex 20 kDa subunit (ARPC4) / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / アクチン / Actin family / アクチン / ATPase, nucleotide binding domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40リピート / WD40リピート / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2 / Actin, alpha skeletal muscle / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 9.0 Å
データ登録者Faessler F / Dimchev G
資金援助 オーストリア, 1件
OrganizationGrant number国
Austrian Science FundP33367 オーストリア
引用ジャーナル: Nat Commun / 年: 2020
タイトル: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction.
著者: Florian Fäßler / Georgi Dimchev / Victor-Valentin Hodirnau / William Wan / Florian K M Schur /
要旨: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves ...The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.
履歴
登録2020年10月22日-
ヘッダ(付随情報) 公開2020年12月2日-
マップ公開2020年12月2日-
更新2024年5月1日-
現状2024年5月1日処理サイト: PDBe / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 0.00404
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（円筒半径に従い着色）
  • 表面レベル: 0.00404
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-7aqk
  • 表面レベル: 0.00404
  • UCSF Chimeraによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • 原子モデルPDB-7aqk
  • Jmolによる作画
  • ダウンロード
ムービービューア
構造ビューアEMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_11869.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_11869.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Structure of the actin filament Arp2/3 complex branch junction
ボクセルのサイズX=Y=Z: 2.137 Å
密度
表面レベル登録者による: 0.00404 / ムービー #1: 0.00404
最小 - 最大-0.0034114548 - 0.014956028
平均 (標準偏差)0.0000346011 (±0.00058454473)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ240240240
Spacing240240240
セルA=B=C: 512.88 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z2.1372.1372.137
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z512.880512.880512.880
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0030.0150.000

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添付データ

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マスク #1

ファイルemd_11869_msk_1.map
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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ハーフマップ: Half map 1

ファイルemd_11869_half_map_1.map
注釈Half map 1
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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ハーフマップ: Half map 2

ファイルemd_11869_half_map_2.map
注釈Half map 2
投影像・断面図
軸ZYX

投影像

断面 (1/2)
密度ヒストグラム

ヒストグラム

ヒストグラム (対数)

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試料の構成要素

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全体 : Actin Filament Arp2/3 Complex Branch Junction

全体名称: Actin Filament Arp2/3 Complex Branch Junction
要素
  • 細胞: Actin Filament Arp2/3 Complex Branch Junction
    • タンパク質・ペプチド: Actin-related protein 2, Arp2
    • タンパク質・ペプチド: Actin-related protein 3, Arp3
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 1b, ArpC1b
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 2, ArpC2
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 3, ArpC3
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 4, ArpC4
    • タンパク質・ペプチド: Actin-related protein 2/3 complex subunit 5, ArpC5
    • タンパク質・ペプチド: Actin, alpha skeletal muscle, ACTA1アクチン

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超分子 #1: Actin Filament Arp2/3 Complex Branch Junction

超分子名称: Actin Filament Arp2/3 Complex Branch Junction / タイプ: cell / ID: 1 / 親要素: 0 / 含まれる分子: all
詳細: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia
由来(天然)生物種: Mus musculus (ハツカネズミ)

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分子 #1: Actin-related protein 2, Arp2

分子名称: Actin-related protein 2, Arp2 / タイプ: protein_or_peptide / ID: 1
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 44.818711 KDa
配列文字列: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP ...文字列:
MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP VYEGFSLPHL TRRLDIAGRD ITRYLIKLLL LRGYAFNHSA DFETVRMIKE KLCYVGYNIE QEQKLALETT VL VESYTLP DGRIIKVGGE RFEAPEALFQ PHLINVEGVG VAELLFNTIQ AADIDTRSEF YKHIVLSGGS TMYPGLPSRL ERE LKQLYL ERVLKGDVEK LSKFKIRIED PPRRKHMVFL GGAVLADIMK DKDNFWMTRQ EYQEKGVRVL EKLGVTVR

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分子 #2: Actin-related protein 3, Arp3

分子名称: Actin-related protein 3, Arp3 / タイプ: protein_or_peptide / ID: 2
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 47.428031 KDa
配列文字列: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI ...文字列:
MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI DSGDGVTHVI PVAEGYVIGS CIKHIPIAGR DITYFIQQLL RDREVGIPPE QSLETAKAVK ERYSYVCPDL VK EFNKYDT DGSKWIKQYT GINAISKKEF SIDVGYERFL GPEIFFHPEF ANPDFTQPIS EVVDEVIQNC PIDVRRPLYK NIV LSGGST MFRDFGRRLQ RDLKRTVDAR LKLSEELSGG RLKPKPIDVQ VITHHMQRYA VWFGGSMLAS TPEFYQVCHT KKDY EEIGP SICRHNPVFG VMS

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分子 #3: Actin-related protein 2/3 complex subunit 1b, ArpC1b

分子名称: Actin-related protein 2/3 complex subunit 1b, ArpC1b
タイプ: protein_or_peptide / ID: 3
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 41.016738 KDa
配列文字列: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGVDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI ...文字列:
MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGVDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI FSAYIKEVEE RPAPTPWGSK MPFGELMFES SSSCGWVHGV CFSANGSRVA WVSHDSTVCL ADADKKMAVA TL ASETLPL LAVTFITESS LVAAGHDCFP VLFTYDSAAG KLSFGGRLDV PKQSSQRGLT ARERFQNLDK KASSEGSAAA GAG LDSLHK NSVSQISVLS GGKAKCSQFC TTGMDGGMSI WDVRSLESAL KDLKIV

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分子 #4: Actin-related protein 2/3 complex subunit 2, ArpC2

分子名称: Actin-related protein 2/3 complex subunit 2, ArpC2 / タイプ: protein_or_peptide / ID: 4
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 34.402043 KDa
配列文字列: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV ...文字列:
MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV FKDDDDVVIG KVFMQEFKEG RRASHTAPQV LFSHREPPLE LKDTDAAVGD NIGYITFVLF PRHTNASARD NT INLIHTF RDYLHYHIKC SKAYIHTRMR AKTSDFLKVL NRARPDAEKK EMKTITGKTF SSR

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分子 #5: Actin-related protein 2/3 complex subunit 3, ArpC3

分子名称: Actin-related protein 2/3 complex subunit 3, ArpC3 / タイプ: protein_or_peptide / ID: 5
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 20.572666 KDa
配列文字列:
MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF MNKSLSGPGQ

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分子 #6: Actin-related protein 2/3 complex subunit 4, ArpC4

分子名称: Actin-related protein 2/3 complex subunit 4, ArpC4 / タイプ: protein_or_peptide / ID: 6
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 19.697047 KDa
配列文字列:
MTATLRPYLS AVRATLQAAL CLENFSSQVV ERHNKPEVEV RSSKELLLQP VTISRNEKEK VLIEGSINSV RVSIAVKQAD EIEKILCHK FMRFMMMRAE NFFILRRKPV EGYDISFLIT NFHTEQMYKH KLVDFVIHFM EEIDKEISEM KLSVNARARI V AEEFLKNF

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分子 #7: Actin-related protein 2/3 complex subunit 5, ArpC5

分子名称: Actin-related protein 2/3 complex subunit 5, ArpC5 / タイプ: protein_or_peptide / ID: 7
詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 1 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 16.295317 KDa
配列文字列:
MSKNTVSSAR FRKVDVDEYD ENKFVDEDDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAVLLQWH EKALAAGGVG SIVRVLTARK TV

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分子 #8: Actin, alpha skeletal muscle, ACTA1

分子名称: Actin, alpha skeletal muscle, ACTA1 / タイプ: protein_or_peptide / ID: 8
詳細: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even ...詳細: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
コピー数: 11 / 光学異性体: LEVO
由来(天然)生物種: Mus musculus (ハツカネズミ)
分子量理論値: 42.096953 KDa
配列文字列: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...文字列:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析サブトモグラム平均法
試料の集合状態cell

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試料調製

緩衝液pH: 6.1
構成要素:
濃度名称
10.0 mMMES
150.0 mMsodium chloride塩化ナトリウム
5.0 mMEGTA
5.0 mMGlucoseグルコース
5.0 mMMagnesium chloride

詳細: Adjust to pH 6.1 using NaOH
グリッドモデル: Quantifoil R2/2 / 材質: GOLD / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 120 sec. / 前処理 - 雰囲気: AIR
詳細: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin
凍結凍結剤: ETHANE / チャンバー内湿度: 80 % / チャンバー内温度: 277 K
詳細: Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials.

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス（公称値）: -0.0055 µm / 最小 デフォーカス（公称値）: -0.00175 µm / 倍率（公称値）: 42000
特殊光学系エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
ホルダー冷却材: NITROGEN
撮影フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)
平均露光時間: 1.21 sec. / 平均電子線量: 2.79 e/Å2
詳細: Images were collected in movie-mode at 7 frames per tilt
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

抽出トモグラム数: 131 / 使用した粒子像数: 39300
参照モデル: Reference generated from manually selected particles
手法: Template Matching
ソフトウェア: (名称: Dynamo (ver. 1.133), Warp (ver. 1.07))
詳細: After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained.
最終 3次元分類クラス数: 1 / 平均メンバー数/クラス: 14296 / ソフトウェア - 名称: RELION (ver. 3.0.9)
最終 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0.9)
詳細: Multiple particle refinement in M version 1.0.9 was performed after 3D Refinement in RELION.
最終 再構成使用したクラス数: 1 / 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 9.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0.9)
詳細: Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9.
使用したサブトモグラム数: 14296
FSC曲線 (解像度の算出)

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原子モデル構築 1

初期モデル
PDB IDChain

1tyq

chain_id: A, residue_range: 2-39, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: A, residue_range: 52-353, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: A, residue_range: 360-418, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: B, residue_range: 151-345, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: C, residue_range: 1-288, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: C, residue_range: 319-372, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: D, residue_range: 1-208, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: D, residue_range: 217-281, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: E, residue_range: 2-150, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: E, residue_range: 155-174, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: F, residue_range: 3-168, source_name: PDB, initial_model_type: experimental model

1tyq

chain_id: G, residue_range: 36-151, source_name: PDB, initial_model_type: experimental model

4jd2

chain_id: B, residue_range: 4-150, source_name: PDB, initial_model_type: experimental model

4jd2

chain_id: B, residue_range: 346-387, source_name: PDB, initial_model_type: experimental model

1k8k

chain_id: C, residue_range: 297-309, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: A, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: B, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: C, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: D, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model

6t20

chain_id: E, residue_range: 5-375, source_name: PDB, initial_model_type: experimental model
精密化空間: REAL / プロトコル: FLEXIBLE FIT
得られたモデル

PDB-7aqk:
Model of the actin filament Arp2/3 complex branch junction in cells

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万見について

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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