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- EMDB-72072: Augmin V junction with NEDD1 (WD) -

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Basic information

Entry
Database: EMDB / ID: EMD-72072
TitleAugmin V junction with NEDD1 (WD)
Map data
Sample
  • Complex: Augmin NEDD1 complex
    • Protein or peptide: AUGMIN subunit 2
    • Protein or peptide: AUGMIN subunit 3
    • Protein or peptide: AUGMIN subunit 5
    • Protein or peptide: AUGMIN subunit 6
    • Protein or peptide: AUGMIN subunit 7
    • Protein or peptide: AUGMIN subunit 8
    • Protein or peptide: Protein NEDD1
KeywordsMicrotubule nucleator / PLANT PROTEIN
Function / homology
Function and homology information


gamma-tubulin complex binding / regulation of phragmoplast microtubule organization / megagametogenesis / microgametogenesis / cell plate assembly / cytokinesis by cell plate formation / phragmoplast microtubule organization / HAUS complex / embryo sac development / regulation of microtubule nucleation ...gamma-tubulin complex binding / regulation of phragmoplast microtubule organization / megagametogenesis / microgametogenesis / cell plate assembly / cytokinesis by cell plate formation / phragmoplast microtubule organization / HAUS complex / embryo sac development / regulation of microtubule nucleation / microtubule minus-end binding / phragmoplast / pollen development / microtubule organizing center organization / kinetochore microtubule / microtubule nucleation / positive regulation of cytokinesis / microtubule organizing center / spindle assembly / regulation of mitotic spindle organization / spindle microtubule / kinetochore / microtubule cytoskeleton organization / spindle / nuclear envelope / mitotic cell cycle / microtubule / cell division / nucleus
Similarity search - Function
Protein NEDD1 / QWRF family / Plant AUGMIN subunit 7 / QWRF family / Plant nuclear matrix protein 1 (NMP1) / AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 ...Protein NEDD1 / QWRF family / Plant AUGMIN subunit 7 / QWRF family / Plant nuclear matrix protein 1 (NMP1) / AUGMIN subunit 5, plant / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 2 / HAUS augmin-like complex subunit 7-like / HAUS augmin-like complex subunit 6 / HAUS augmin-like complex subunit 6, N-terminal / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 6 N-terminus / HAUS augmin-like complex subunit 5 / HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3 / WD domain, G-beta repeat / Trp-Asp (WD) repeats signature. / 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
Protein NEDD1 / AUGMIN subunit 2 / AUGMIN subunit 3 / AUGMIN subunit 7 / AUGMIN subunit 6 / AUGMIN subunit 5 / AUGMIN subunit 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsAshaduzzaman M / Al-Bassam J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Augmin(top) with NEDD1 (wd40)
Authors: Ashaduzzaman M / Al-Bassam J
History
DepositionAug 11, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72072.png

Downloads & links

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Map

FileDownload / File: emd_72072.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 180 pix.
= 316.8 Å		1.76 Å/pix.
x 180 pix.
= 316.8 Å		1.76 Å/pix.
x 180 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.00031055632 - 2.3017747
Average (Standard dev.)0.0038762274 (±0.04471827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72072_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72072_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Augmin NEDD1 complex

EntireName: Augmin NEDD1 complex
Components
  • Complex: Augmin NEDD1 complex
    • Protein or peptide: AUGMIN subunit 2
    • Protein or peptide: AUGMIN subunit 3
    • Protein or peptide: AUGMIN subunit 5
    • Protein or peptide: AUGMIN subunit 6
    • Protein or peptide: AUGMIN subunit 7
    • Protein or peptide: AUGMIN subunit 8
    • Protein or peptide: Protein NEDD1

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Supramolecule #1: Augmin NEDD1 complex

SupramoleculeName: Augmin NEDD1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: AUGMIN subunit 2

MacromoleculeName: AUGMIN subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.952092 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SDALSIASDL GFAVAPPPSQ EELQSFASSN GERGDDLIRV LRELSVVQRK IADLQVELQG RKDDKNVAHL THVGEMQKKI ETLSRITQI LKDVIQNKDR IIARLQQPYS LDCIPVEAEY QKQFSELLMK AASDYGALTA SVSDFQWSQS MQG

UniProtKB: AUGMIN subunit 2

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Macromolecule #2: AUGMIN subunit 3

MacromoleculeName: AUGMIN subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 69.809453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSARLCSLV AELGYEGAGK LDPDSFEWPF QYDDARPILD WICSSLRPSN VLSLAELSLY EQFQRDGKLL EGDDLDQAYD SISAFSSRR NNQEAVFGAE ESIKEVRDAT LAHKAEALEL QRQLRRLQTQ YDLLTGQSSA LIQGRRARVA ATSAVSGQIT A IEDSLSAR ...String:
MSSARLCSLV AELGYEGAGK LDPDSFEWPF QYDDARPILD WICSSLRPSN VLSLAELSLY EQFQRDGKLL EGDDLDQAYD SISAFSSRR NNQEAVFGAE ESIKEVRDAT LAHKAEALEL QRQLRRLQTQ YDLLTGQSSA LIQGRRARVA ATSAVSGQIT A IEDSLSAR NLQMNGVLGR LASTSQELAH YHSGEEDGIY LAYSDFHAYL AGDSACTKEL NQWFAKQLDT GPYRLVAEEG KS KCSWVSL DDTSNMLRDL EKSQHQRVAE LQRLRSIFGT SERQWIEAQV ENAKQQAILL TLKSQVTSVE AHIHFDLHSL RRK HADLVE EISTLYQKEE KLLSETIPEL CWELAQLQDT YILQGDYDLK VMRQELYISK QKVFINHLVN QLARHQFLKL ACQL EKKNM LGAFSLLKVI ESELQGYLSA TRSRVGRCSA LIQAASDVQE QGAVDDRDSF LHGVRDLLSI HSNTQAGLST YVSAP AIIQ QIVALQSDLS SLQSDLENSL PDDRNRCINE LCTHIQNLQQ LLFASSTTAQ PILTPWPLMK ELDEMGKINS KLSTAV EEV TLEHRNKREI VKHHAKDVEL QRRVFVDFFC NPERLRNQVR ELNALVRARQ ASSS

UniProtKB: AUGMIN subunit 3

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Macromolecule #3: AUGMIN subunit 5

MacromoleculeName: AUGMIN subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 87.230984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQSLSSSAPT PEAILEWLQK EMGYRQLGPY NGSSKSHVPS IDAIRKICRG NMIPIWNFLI NRVKSEKTVE RIRRNITVHG GSSNASIGS SVNPGKEESK SKGRRKDKTV TGESSSYAED REAALQEREL AAKEVERLRN IVRRQRKDLK ARMLEVSREE A ERKRMLDE ...String:
MQSLSSSAPT PEAILEWLQK EMGYRQLGPY NGSSKSHVPS IDAIRKICRG NMIPIWNFLI NRVKSEKTVE RIRRNITVHG GSSNASIGS SVNPGKEESK SKGRRKDKTV TGESSSYAED REAALQEREL AAKEVERLRN IVRRQRKDLK ARMLEVSREE A ERKRMLDE RANYRHKQAL LEAYDQQCDE ATRIFAEYHK RLQVYVNQAN DAQRSVNSSN EVLSSLSANS EREAVYSTVK GT KSADDVI LMETTRERNI RIVCDLLASR MIERIRNSFP AYEGNGICSL PELETAKLGF EYDGEITDEM KTVIVNSLRG PPL LLQAIA AYTLRIKTLI SREMEKIDVR ADAEMLRYKF ENNRVTDNSS SDVSSPSNNQ LLERQKAHVQ QFLATEDALN KAAE ARDLC HKFINRLHGS ADTATHSFVG GTTQSGSNLR QFELDVWGKE REAAGLRASL NTLLSEIQRL NKLCAERKEA EDSLK KKWK KIEEFDARRS ELETIYTTLL KANMDAVAFW NQQPLAAREY ASATVIPASE VVVDISNSAK DFIEKEVSAF FQSPDN SLY MLPATPQGLL ESMGANGSTG PEAVAYAEKN AALLTARAGA RDPSAIPSIC RISAALQYPA GLEGSDASLA SVLESLE FC LRVRGSEACV LEDLAKAIDL VHIRQDLVES GHSLLDHAFR AQQKYERTTN YCLDLASEQE NTISDQWLPE LRTAVQNA Q ASSEHCKYVR GLLDEWWEQP ASTVVDWVTV DGQSVAAWQN HVKQLLAFYD KESLRT

UniProtKB: AUGMIN subunit 5

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Macromolecule #4: AUGMIN subunit 6

MacromoleculeName: AUGMIN subunit 6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 36.708531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTMDREKERE LELESAMYTN CLLLGLDPNV IGLGASNGTP RVGLFRHSNP KLGEQLLYFI LSSLRGPAQS SKDFDKVWPI FDSAQSRDF RKVVQAIISE LESQGALPRS NSRVSSLATC CGPRFVELLW QLSLHALREV HRRTFPADVA SNPLPSSLTD V SFSHAATL ...String:
MTMDREKERE LELESAMYTN CLLLGLDPNV IGLGASNGTP RVGLFRHSNP KLGEQLLYFI LSSLRGPAQS SKDFDKVWPI FDSAQSRDF RKVVQAIISE LESQGALPRS NSRVSSLATC CGPRFVELLW QLSLHALREV HRRTFPADVA SNPLPSSLTD V SFSHAATL LPVTKARIVL ERRRFLKNAE TAVQRQAMWS NLAHEMTAEF RGLCAEEAYL QQELEKLNDL RNKVKQEGEV WD DLVSSSS QNSHLVSKAT RLWDSIMARK GQHEVLASGP IEDLIAHREH RYRISGSALL AAMDQSSQVP RAELLSAHSD DSA SLADDK EL

UniProtKB: AUGMIN subunit 6

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Macromolecule #5: AUGMIN subunit 7

MacromoleculeName: AUGMIN subunit 7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 37.046961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAKQMEEIQ KKLRLLSYPR ANAPAQSLLF AGMERYALLE WLFFKLLGDK SPFSQQNLQG DAGVRDEETV RIQYLAEIAK FLGITPTVD IEAIQGHGTY EDRMEMLRNI VDLVEASLFS DNQEWSIDEQ VAKDIQLIDA IAERQSLIFS EECKLFPADV Q IQSIYPLP ...String:
MAAKQMEEIQ KKLRLLSYPR ANAPAQSLLF AGMERYALLE WLFFKLLGDK SPFSQQNLQG DAGVRDEETV RIQYLAEIAK FLGITPTVD IEAIQGHGTY EDRMEMLRNI VDLVEASLFS DNQEWSIDEQ VAKDIQLIDA IAERQSLIFS EECKLFPADV Q IQSIYPLP DVSELETKLS EQAKILSNLQ QKVDDLAAKH AYNPDEEYTE VESQLRARLE SFLETARAFN TIYTKEIRPW TH MMEVPQL HGFGPAANRL LEAYNMLLKF LGNLKNLRDS HAALSIGSSG TVAGEPSSVT RIVSDCEAAL TVLNRDLGIL SAS IAREQG ERL

UniProtKB: AUGMIN subunit 7

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Macromolecule #6: AUGMIN subunit 8

MacromoleculeName: AUGMIN subunit 8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 18.65833 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EDVHQLRLLH NRYLQWRFAI ARAESVMYIQ RLTSEETLFN VWHAISELQD HVTRQRIGLQ QLKLEIKLNS LLNDQMVSLE DWATLERDH VSSLVGAISD LEANTLRLPA TGGTKADTES LKAAMSSALD VMQAMGSSIW SLLSKVEEMN IMVTELAVVV T KESSM

UniProtKB: AUGMIN subunit 8

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Macromolecule #7: Protein NEDD1

MacromoleculeName: Protein NEDD1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 33.256484 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: WRLLAASGGD TVKLFDVSAD SGDPCVLSYT PSPGCAVNSV KWNHTNLVVA STGEDKKISL WRKNGQSLGT VPVTGKDGGD SAEECLSAI SFSKKGSRYI CSGGTGQIVK IWDLQRKLCI KKLKGHTSTI TGVMYNCKDE HLASVSVGGD LIVHNLASGA R ATELKDPN ...String:
WRLLAASGGD TVKLFDVSAD SGDPCVLSYT PSPGCAVNSV KWNHTNLVVA STGEDKKISL WRKNGQSLGT VPVTGKDGGD SAEECLSAI SFSKKGSRYI CSGGTGQIVK IWDLQRKLCI KKLKGHTSTI TGVMYNCKDE HLASVSVGGD LIVHNLASGA R ATELKDPN GQVLRLLDYS RSSRHLLVTA GDDGTVHLWD TTGRSPKMSW LKQHSAPTAG VCFSPSNEKI IASVGMDKKL YT YDSGSRR SSSCIAYEAP FSSLAFGDNG YILVAGTSNG RVVFYDIRGK PQPVTVLHAF SNSEDVTSLS WQT

UniProtKB: Protein NEDD1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 0.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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