[English] 日本語
Yorodumi
- EMDB-22416: Cryo-EM structure of Arpin-bound Arp2/3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22416
TitleCryo-EM structure of Arpin-bound Arp2/3 complex
Map dataMap of bovine Arp2/3 complex with Arpin CA peptide. Postprocessed with deepEMhancer
Sample
  • Complex: bovine Arp2/3 complex with Arpin
    • Complex: bovine Arp2/3
      • Protein or peptide: Actin-related protein 3
      • Protein or peptide: Actin-related protein 2
      • Protein or peptide: Actin-related protein 2/3 complex subunit 1B
      • Protein or peptide: Actin-related protein 2/3 complex subunit 2
      • Protein or peptide: Actin-related protein 2/3 complex subunit 3
      • Protein or peptide: Actin-related protein 2/3 complex subunit 4
      • Protein or peptide: Actin-related protein 2/3 complex subunit 5
    • Complex: Arpin
      • Protein or peptide: Arpin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsactin / ATPase / actin related protein / arp / cytoskeleton / Arp2-3 complex / actin nucleation / actin branching / CONTRACTILE PROTEIN / Arpin
Function / homology
Function and homology information


negative regulation of actin nucleation / negative regulation of lamellipodium morphogenesis / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / directional locomotion / regulation of actin filament polymerization / Clathrin-mediated endocytosis ...negative regulation of actin nucleation / negative regulation of lamellipodium morphogenesis / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / directional locomotion / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of double-strand break repair via homologous recombination / cilium assembly / positive regulation of lamellipodium assembly / actin filament polymerization / negative regulation of cell migration / cell projection / structural constituent of cytoskeleton / actin filament binding / cell migration / lamellipodium / site of double-strand break / neuron projection / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Arpin / Arp2/3-interacting proteins Arpin / 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 ...Arpin / Arp2/3-interacting proteins Arpin / 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) / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin-related protein 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B / Arpin
Similarity search - Component
Biological speciesBos taurus (cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
Authorsvan Eeuwen T / Fregoso FE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM07391 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008275 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F31-HL146077 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular mechanism of Arp2/3 complex inhibition by Arpin.
Authors: Fred E Fregoso / Trevor van Eeuwen / Gleb Simanov / Grzegorz Rebowski / Malgorzata Boczkowska / Austin Zimmet / Alexis M Gautreau / Roberto Dominguez /
Abstract: Positive feedback loops involving signaling and actin assembly factors mediate the formation and remodeling of branched actin networks in processes ranging from cell and organelle motility to ...Positive feedback loops involving signaling and actin assembly factors mediate the formation and remodeling of branched actin networks in processes ranging from cell and organelle motility to mechanosensation. The Arp2/3 complex inhibitor Arpin controls the directional persistence of cell migration by interrupting a feedback loop involving Rac-WAVE-Arp2/3 complex, but Arpin's mechanism of inhibition is unknown. Here, we describe the cryo-EM structure of Arpin bound to Arp2/3 complex at 3.24-Å resolution. Unexpectedly, Arpin binds Arp2/3 complex similarly to WASP-family nucleation-promoting factors (NPFs) that activate the complex. However, whereas NPFs bind to two sites on Arp2/3 complex, on Arp2-ArpC1 and Arp3, Arpin only binds to the site on Arp3. Like NPFs, Arpin has a C-helix that binds at the barbed end of Arp3. Mutagenesis studies in vitro and in cells reveal how sequence differences within the C-helix define the molecular basis for inhibition by Arpin vs. activation by NPFs.
History
DepositionAug 9, 2020-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jpn
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_22416.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of bovine Arp2/3 complex with Arpin CA peptide. Postprocessed with deepEMhancer
Voxel sizeX=Y=Z: 0.836 Å
Density
Contour LevelBy AUTHOR: 0.154 / Movie #1: 0.154
Minimum - Maximum-0.0017322488 - 1.6263168
Average (Standard dev.)0.001566827 (±0.02819422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8360.8360.836
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z267.520267.520267.520
α/β/γ90.00090.00090.000
start NX/NY/NZ838693
NX/NY/NZ155149226
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0021.6260.002

-
Supplemental data

-
Additional map: Map of bovine Arp2/3 complex with Arpin CA...

Fileemd_22416_additional_1.map
AnnotationMap of bovine Arp2/3 complex with Arpin CA peptide. B factor sharpend and postprocessed with deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half map 2 of bovine Arp2/3 complex with Arpin CA peptide.

Fileemd_22416_half_map_1.map
AnnotationHalf map 2 of bovine Arp2/3 complex with Arpin CA peptide.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half map 1 of bovine Arp2/3 complex with Arpin CA peptide.

Fileemd_22416_half_map_2.map
AnnotationHalf map 1 of bovine Arp2/3 complex with Arpin CA peptide.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : bovine Arp2/3 complex with Arpin

EntireName: bovine Arp2/3 complex with Arpin
Components
  • Complex: bovine Arp2/3 complex with Arpin
    • Complex: bovine Arp2/3
      • Protein or peptide: Actin-related protein 3
      • Protein or peptide: Actin-related protein 2
      • Protein or peptide: Actin-related protein 2/3 complex subunit 1B
      • Protein or peptide: Actin-related protein 2/3 complex subunit 2
      • Protein or peptide: Actin-related protein 2/3 complex subunit 3
      • Protein or peptide: Actin-related protein 2/3 complex subunit 4
      • Protein or peptide: Actin-related protein 2/3 complex subunit 5
    • Complex: Arpin
      • Protein or peptide: Arpin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

+
Supramolecule #1: bovine Arp2/3 complex with Arpin

SupramoleculeName: bovine Arp2/3 complex with Arpin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 248.9 KDa

+
Supramolecule #2: bovine Arp2/3

SupramoleculeName: bovine Arp2/3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7
Source (natural)Organism: Bos taurus (cattle) / Organ: brain

+
Supramolecule #3: Arpin

SupramoleculeName: Arpin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human) / Strain: BL21 (DE3)

+
Macromolecule #1: Actin-related protein 3

MacromoleculeName: Actin-related protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 46.908355 KDa
SequenceString: GRLPACVVDC GTGYTKLGYA GNTEPQFIIP SCIAIKESAK VGDQAQRRVM KGVDDLDFFI GDEAIEKPTY ATKWPIRHGI VEDWDLMER FMEQVIFKYL RAEPEDHYFL LTEPPLNTPE NREYTAEIMF ESFNVPGLYI AVQAVLALAA SWTSRQVGER T LTGTVIDS ...String:
GRLPACVVDC GTGYTKLGYA GNTEPQFIIP SCIAIKESAK VGDQAQRRVM KGVDDLDFFI GDEAIEKPTY ATKWPIRHGI VEDWDLMER FMEQVIFKYL RAEPEDHYFL LTEPPLNTPE NREYTAEIMF ESFNVPGLYI AVQAVLALAA SWTSRQVGER T LTGTVIDS GDGVTHVIPV AEGYVIGSCI KHIPIAGRDI TYFIQQLLRD REVGIPPEQS LETAKAVKER YSYVCPDLVK EF NKYDTDG SKWIKQYTGI NAISKKEFSI DVGYERFLGP EIFFHPEFAN PDFTQPISEV VDEVIQNCPI DVRRPLYKNI VLS GGSTMF RDFGRRLQRD LKRTVDARLK LSEELSGGRL KPKPIDVQVI THHMQRYAVW FGGSMLASTP EFYQVCHTKK DYEE IGPSI CRHNPVFG

UniProtKB: Actin-related protein 3

+
Macromolecule #2: Actin-related protein 2

MacromoleculeName: Actin-related protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 42.945453 KDa
SequenceString: QGRKVVVCDN GTGFVKCGYA GSNFPEHIFP ALVGRPIIRS TTKVGNIEIK DLMVGDEASE LRSMLEVNYP MENGIVRNWD DMKHLWDYT FGPEKLNIDT RNCKILLTEP PMNPTKNREK IVEVMFETYQ FSGVYVAIQA VLTLYAQGLL TGVVVDSGDG V THICPVYE ...String:
QGRKVVVCDN GTGFVKCGYA GSNFPEHIFP ALVGRPIIRS TTKVGNIEIK DLMVGDEASE LRSMLEVNYP MENGIVRNWD DMKHLWDYT FGPEKLNIDT RNCKILLTEP PMNPTKNREK IVEVMFETYQ FSGVYVAIQA VLTLYAQGLL TGVVVDSGDG V THICPVYE GFSLPHLTRR LDIAGRDITR YLIKLLLLRG YAFNHSADFE TVRMIKEKLC YVGYNIEQEQ KLALETTVLV ES YTLPDGR IIKVGGERFE APEALFQPHL INVEGVGVAE LLFNTIQAAD IDTRSEFYKH IVLSGGSTMY PGLPSRLERE LKQ LYLERV LKGDVEKLSK FKIRIEDPPR RKHMVFLGGA VLADIMKDKD NFWMTRQEYQ E

UniProtKB: Actin-related protein 2

+
Macromolecule #3: Actin-related protein 2/3 complex subunit 1B

MacromoleculeName: Actin-related protein 2/3 complex subunit 1B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 41.030766 KDa
SequenceString: MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGIDW APDSNRIVTC GTDRNAYVWT LKGRTWKPT LVILRINRAA RCVRWAPNEK KFAVGSGSRV ISICYFEQEN DWWVCKHIKK PIRSTVLSLD WHPNSVLLAA G SCDFKCRI ...String:
MAYHSFLVEP ISCHAWNKDR TQIAICPNNH EVHIYEKSGN KWVQVHELKE HNGQVTGIDW 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

UniProtKB: Actin-related protein 2/3 complex subunit 1B

+
Macromolecule #4: Actin-related protein 2/3 complex subunit 2

MacromoleculeName: Actin-related protein 2/3 complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 34.402043 KDa
SequenceString: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV ...String:
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

UniProtKB: Actin-related protein 2/3 complex subunit 2

+
Macromolecule #5: Actin-related protein 2/3 complex subunit 3

MacromoleculeName: Actin-related protein 2/3 complex subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 20.572666 KDa
SequenceString:
MPAYHSSLMD PDTKLIGNMA LLPIRSQFKG PAPRETKDTD IVDEAIYYFK ANVFFKNYEI KNEADRTLIY ITLYISECLK KLQKCNSKS QGEKEMYTLG ITNFPIPGEP GFPLNAIYAK PANKQEDEVM RAYLQQLRQE TGLRLCEKVF DPQNDKPSKW W TCFVKRQF MNKSLSGPGQ

UniProtKB: Actin-related protein 2/3 complex subunit 3

+
Macromolecule #6: Actin-related protein 2/3 complex subunit 4

MacromoleculeName: Actin-related protein 2/3 complex subunit 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 19.697047 KDa
SequenceString:
MTATLRPYLS AVRATLQAAL CLENFSSQVV ERHNKPEVEV RSSKELLLQP VTISRNEKEK VLIEGSINSV RVSIAVKQAD EIEKILCHK FMRFMMMRAE NFFILRRKPV EGYDISFLIT NFHTEQMYKH KLVDFVIHFM EEIDKEISEM KLSVNARARI V AEEFLKNF

UniProtKB: Actin-related protein 2/3 complex subunit 4

+
Macromolecule #7: Actin-related protein 2/3 complex subunit 5

MacromoleculeName: Actin-related protein 2/3 complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 15.473396 KDa
SequenceString:
ARFRKVDVDE YDENKFVDEE DGGDGQAGPD EGEVDSCLRQ GNMTAALQAA LKNPPINTKS QAVKDRAGSI VLKVLISFKA NDIEKAVQS LDKNGVDLLM KYIYKGFESP SDNSSAVLLQ WHEKALAAGG VGSIVRVLTA RKTV

UniProtKB: Actin-related protein 2/3 complex subunit 5

+
Macromolecule #8: Arpin

MacromoleculeName: Arpin / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.730892 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ASWTDNIMAQ KCSKGAAAEI REQGDGAEDE EWDD

UniProtKB: Arpin

+
Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
1.0 mMHSCH2CH(OH)CH(OH)CH2SHDithiothreitol
0.2 mMC10H14N5O13P3Na2Adenosine triphosphate disodium salt
0.2 mMMgCl2magnesium chloride
GridPretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: unspecified
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC
Details: Grids were manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged using a Leica EM CPC manual plunger..
DetailsThis sample was monodisperse.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
DetailsData were collected in super-resolution mode with an illuminated area of 1.01 um, nominal dose of 40 e-/A^2, a dose rate of 4.87 e-/s/pixel, and 2 or 5 exposures per hole by image shift.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 9661 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsSuper resolution mode; micrographs binned during motion correction
Particle selectionNumber selected: 4485066 / Details: Particles autopicked in cryoSPARC
Startup modelType of model: OTHER / Details: ab initio model generated by cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 182324
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4)
Final 3D classificationNumber classes: 6 / Avg.num./class: 150000 / Software - Name: cryoSPARC (ver. 2.12.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

source_name: PDB, initial_model_type: experimental model

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 132 / Target criteria: correlation
Output model

PDB-7jpn:
Cryo-EM structure of Arpin-bound Arp2/3 complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more