[English] 日本語
Yorodumi
- EMDB-63642: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63642
TitleStructure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex)
Map dataStitched composite map
Sample
  • Complex: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsSPIN90 / actin / cytoskeleton / Arp2-3 complex / Nucleation Promoting Factor / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


muscle cell projection membrane / 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 / Arp2/3 complex binding / Striated Muscle Contraction / regulation of actin filament polymerization / Clathrin-mediated endocytosis ...muscle cell projection membrane / 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 / Arp2/3 complex binding / Striated Muscle Contraction / regulation of actin filament polymerization / Clathrin-mediated endocytosis / intermediate filament / Neutrophil degranulation / positive regulation of actin filament polymerization / striated muscle thin filament / skeletal muscle thin filament assembly / regulation of postsynapse assembly / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / cytoskeletal protein binding / skeletal muscle fiber development / stress fiber / actin filament polymerization / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / cell projection / FCGR3A-mediated phagocytosis / actin filament / positive regulation of neuron projection development / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / SH3 domain binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / actin filament binding / synaptic vesicle membrane / cell migration / site of double-strand break / lamellipodium / actin cytoskeleton / actin binding / cell cortex / neuron projection / hydrolase activity / postsynapse / endosome / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / 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 ...SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / 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 20 kDa subunit (ARPC4) / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / ATPase, nucleotide binding domain / Src homology 3 (SH3) domain profile. / SH3 domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 3 / Actin, alpha skeletal muscle / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B / NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsFrancis J / Pathri AK / Chowdhury S
Funding support India, 2 items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)FBR070301 India
Council of Scientific & Industrial Research (CSIR)OLP0028 India
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation.
Authors: Francis J / Pathri AK / Shyam KT / Sripada S / Mitra R / Narvaez-Ortiz HY / Eliyan KV / Nolen BJ / Chowdhury S
History
DepositionMar 5, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63642.png

Downloads & links

-
Map

FileDownload / File: emd_63642.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStitched composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.13610071 - 1.373971
Average (Standard dev.)0.019757712 (±0.04298153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63642_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened consensus map

Fileemd_63642_additional_1.map
AnnotationSharpened consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened consensus map

Fileemd_63642_additional_2.map
AnnotationUnsharpened consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Consensus Odd half map

Fileemd_63642_half_map_1.map
AnnotationConsensus Odd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Consensus Even half map

Fileemd_63642_half_map_2.map
AnnotationConsensus Even half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament...

EntireName: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
Components
  • Complex: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
    • 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
    • Protein or peptide: NCK-interacting protein with SH3 domain
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament...

SupramoleculeName: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 100 KDa

+
Macromolecule #1: Actin-related protein 3

MacromoleculeName: Actin-related protein 3 / type: protein_or_peptide / ID: 1
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 47.428031 KDa
SequenceString: MAGRLPACVV DCGTGYTKLG YAGNTEPQFI IPSCIAIKES AKVGDQAQRR VMKGVDDLDF FIGDEAIEKP TYATKWPIRH GIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG E RTLTGTVI ...String:
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

UniProtKB: Actin-related protein 3

+
Macromolecule #2: Actin-related protein 2

MacromoleculeName: Actin-related protein 2 / type: protein_or_peptide / ID: 2
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 44.818711 KDa
SequenceString: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP ...String:
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

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
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic 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
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic 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
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic 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
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic 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
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 16.251308 KDa
SequenceString:
MSKNTVSSAR FRKVDVGEYD ENKFVDEEDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAVLLQWH EKALAAGGVG SIVRVLTARK TV

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

+
Macromolecule #8: NCK-interacting protein with SH3 domain

MacromoleculeName: NCK-interacting protein with SH3 domain / type: protein_or_peptide / ID: 8
Details: This is a truncated construct of human SPIN90 protein that range from residues 269-722. Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.561293 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EPPAEEEVAT GTTSASDDLE ALGTLSLGTT EEKAAAEAAV PRTIGAELME LVRRNTGLSH ELCRVAIGII VGHIQASVPA SSPVMEQVL LSLVEGKDLS MALPSGQVCH DQQRLEVIFA DLARRKDDAQ QRSWALYEDE GVIRCYLEEL LHILTDADPE V CKKMCKRN ...String:
EPPAEEEVAT GTTSASDDLE ALGTLSLGTT EEKAAAEAAV PRTIGAELME LVRRNTGLSH ELCRVAIGII VGHIQASVPA SSPVMEQVL LSLVEGKDLS MALPSGQVCH DQQRLEVIFA DLARRKDDAQ QRSWALYEDE GVIRCYLEEL LHILTDADPE V CKKMCKRN EFESVLALVA YYQMEHRASL RLLLLKCFGA MCSLDAAIIS TLVSSVLPVE LARDMQTDTQ DHQKLCYSAL IL AMVFSMG EAVPYAHYEH LGTPFAQFLL NIVEDGLPLD TTEQLPDLCV NLLLALNLHL PAADQNVIMA ALSKHANVKI FSE KLLLLL NRGDDPVRIF KHEPQPPHSV LKFLQDVFGS PATAAIFYHT DMMALIDITV RHIADLSPGD KLRMEYLSLM HAIV RTTPY LQHRHRLPDL QAILRRILNE EETSPQCQMD RMIVREMCKE FLVLGEAPS

UniProtKB: NCK-interacting protein with SH3 domain

+
Macromolecule #9: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 9
Details: Residue 75 is 4-methyl-histidine (HIC). It is a post-translation modification. Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 3 / Number real images: 24000 / Average exposure time: 7.19 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction from Cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 28368
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7tpt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9m5e:
Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet 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://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