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- EMDB-72081: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine a... -

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Basic information

Entry
Database: EMDB / ID: EMD-72081
TitleNative GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Map data
Sample
  • Complex: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
    • Protein or peptide: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsligand-gated ion channel / NMDA / antibody / native / TRANSPORT PROTEIN
Function / homology
Function and homology information


Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / regulation of cAMP/PKA signal transduction / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration ...Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / regulation of cAMP/PKA signal transduction / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / sensitization / olfactory learning / dendritic branch / fear response / conditioned taste aversion / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / regulation of respiratory gaseous exchange / apical dendrite / transmitter-gated monoatomic ion channel activity / suckling behavior / interleukin-1 receptor binding / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / negative regulation of dendritic spine maintenance / heterocyclic compound binding / neurotransmitter receptor complex / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / positive regulation of glutamate secretion / transport vesicle membrane / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of synapse assembly / protein heterotetramerization / response to morphine / small molecule binding / glycine binding / receptor clustering / startle response / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / regulation of MAPK cascade / monoatomic ion channel complex / behavioral response to pain / regulation of postsynaptic membrane potential / monoatomic cation transmembrane transport / action potential / positive regulation of calcium ion transport into cytosol / extracellularly glutamate-gated ion channel activity / associative learning / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / monoatomic cation transport / glutamate receptor binding / detection of mechanical stimulus involved in sensory perception of pain / social behavior / ligand-gated monoatomic ion channel activity / positive regulation of synaptic transmission / phosphatase binding / long-term memory / prepulse inhibition / postsynaptic density, intracellular component / behavioral fear response / monoatomic cation channel activity / synaptic cleft / calcium ion homeostasis / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / D2 dopamine receptor binding / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / sensory perception of pain / excitatory synapse / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / regulation of neuron apoptotic process / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / protein tyrosine kinase binding / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / sodium ion transmembrane transport / protein serine/threonine kinase binding / learning / response to amphetamine / synaptic membrane / adult locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.36 Å
AuthorsKim J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Cryo-EM of autoantibody-bound NMDA receptors reveals antigenic hotspots in an active immunization model of anti-NMDAR encephalitis.
Authors: Junhoe Kim / Farzad Jalali-Yazdi / Brian E Jones / Gary L Westbrook / Eric Gouaux /
Abstract: Autoantibodies targeting synaptic membrane proteins are associated with autoimmune encephalitis manifested by seizures, psychosis, and memory dysfunction. Anti--methyl-d-aspartate receptor (NMDAR) ...Autoantibodies targeting synaptic membrane proteins are associated with autoimmune encephalitis manifested by seizures, psychosis, and memory dysfunction. Anti--methyl-d-aspartate receptor (NMDAR) encephalitis, a prototype of these autoimmune synaptic disorders, is unexpectedly common. Unfortunately, how the native repertoire of anti-NMDAR autoantibodies recognizes NMDARs and the precise locations of antigenic epitopes remain poorly understood. Here, we used an active immunization model that closely mimics the human disease to immunize adult mice with intact GluN1/GluN2A receptors, resulting in fulminant autoimmune encephalitis. Serum was collected at 6 weeks postimmunization for single-particle cryo-electron microscopy of GluN1/GluN2A receptors complexed with purified polyclonal anti-NMDAR autoantibody fragments. Native autoantibodies recognized two distinct binding sites on the GluN1 amino-terminal domain, which we confirmed using monoclonal antibodies bound to native NMDARs purified from mouse brain. Structural analysis of autoantibody-bound NMDAR complexes identified antigenic hotspots within the GluN1 amino-terminal domain. These hotspots provide potential targets for therapeutic intervention.
History
DepositionAug 11, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72081.png

Downloads & links

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Map

FileDownload / File: emd_72081.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 336 pix.
= 468.384 Å		1.39 Å/pix.
x 336 pix.
= 468.384 Å		1.39 Å/pix.
x 336 pix.
= 468.384 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.394 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.03798007 - 0.0948815
Average (Standard dev.)0.00016686859 (±0.0034738695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 468.38403 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpen map

Fileemd_72081_additional_1.map
AnnotationSharpen map
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Half map: #2

Fileemd_72081_half_map_1.map
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Half map: #1

Fileemd_72081_half_map_2.map
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Sample components

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Entire : Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine a...

EntireName: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Components
  • Complex: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
    • Protein or peptide: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine a...

SupramoleculeName: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 617 KDa

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Macromolecule #1: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11

MacromoleculeName: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.432527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA QGQMQQSGAE LVKPGASVKL SCKTSGFSFS TSYINWLKQK PGQSLEWIAW IYAGTDGTSY NQKFTDKAQ LTVDTSSSTA YMQFSSLTTD DSAIYYCARE GIYYGNYAGF TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA Q TNSMVTLG ...String:
MVSAIVLYVL LAAAAHSAFA QGQMQQSGAE LVKPGASVKL SCKTSGFSFS TSYINWLKQK PGQSLEWIAW IYAGTDGTSY NQKFTDKAQ LTVDTSSSTA YMQFSSLTTD DSAIYYCARE GIYYGNYAGF TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA Q TNSMVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK LV PRGSAAA AGTGSGGGDY KDHDGDYKDH DIDYKDDDDK

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Macromolecule #2: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11

MacromoleculeName: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.909961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA DIVMTQSPSS LAVTAGEKVT MRCKSSQSLL WSVNQNNYLS WYQQKQGQPP KLLIYGASIR ESWVPDRFT GSGSGTDFTL TISNVHAEDL AVYYCQHNHG SFLPYTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS V VCFLNNFY ...String:
MVSAIVLYVL LAAAAHSAFA DIVMTQSPSS LAVTAGEKVT MRCKSSQSLL WSVNQNNYLS WYQQKQGQPP KLLIYGASIR ESWVPDRFT GSGSGTDFTL TISNVHAEDL AVYYCQHNHG SFLPYTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS V VCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RN ECSN

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Macromolecule #3: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 105.61782 KDa
SequenceString: MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS ...String:
MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS DDHEGRAAQK RLETLLEERE SKAEKVLQFD PGTKNVTALL MEARDLEARV IILSASEDDA ATVYRAAAML NM TGSGYVW LVGEREISGN ALRYAPDGII GLQLINGKNE SAHISDAVGV VAQAVHELLE KENITDPPRG CVGNTNIWKT GPL FKRVLM SSKYADGVTG RVEFNEDGDR KFANYSIMNL QNRKLVQVGI YNGTHVIPND RKIIWPGGET EKPRGYQMST RLKI VTIHQ EPFVYVKPTM SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCVDLLIK LARTMNFTYE VHLVA DGKF GTQERVNNSN KKEWNGMMGE LLSGQADMIV APLTINNERA QYIEFSKPFK YQGLTILVKK EIPRSTLDSF MQPFQS TLW LLVGLSVHVV AVMLYLLDRF SPFGRFKVNS EEEEEDALTL SSAMWFSWGV LLNSGIGEGA PRSFSARILG MVWAGFA MI IVASYTANLA AFLVLDRPEE RITGINDPRL RNPSDKFIYA TVKQSSVDIY FRRQVELSTM YRHMEKHNYE SAAEAIQA V RDNKLHAFIW DSAVLEFEAS QKCDLVTTGE LFFRSGFGIG MRKDSPWKQN VSLSILKSHE NGFMEDLDKT WVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQMQL AFAAVNVWRK NLQDRKSGRA EPDPKKKATF RAITSTLAS SFKRRRSSKD TSTGGGRGAL QNQKDTVLPR RAIEREEGQL QLCSRHRES

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #4: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 166.162062 KDa
SequenceString: MKPSAECCSP KFWLVLAVLA VSGSKARSQK SAPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVL ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI ...String:
MKPSAECCSP KFWLVLAVLA VSGSKARSQK SAPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVL ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI FSIVTTYFPG YQDFVNKIRS TIENSFVGWE LEEVLLLDMS LDDGDSKIQN QLKKLQSPII LLYCTKEEAT YI FEVANSV GLTGYGYTWI VPSLVAGDTD TVPSEFPTGL ISVSYDEWDY GLPARVRDGI AIITTAASDM LSEHSFIPEP KSS CYNTHE KRIYQSNMLN RYLINVTFEG RNLSFSEDGY QMHPKLVIIL LNKERKWERV GKWKDKSLQM KYYVWPRMCP ETEE QEDDH LSIVTLEEAP FVIVESVDPL SGTCMRNTVP CQKRIISENK TDEEPGYIKK CCKGFCIDIL KKISKSVKFT YDLYL VTNG KHGKKINGTW NGMIGEVVMK RAYMAVGSLT INEERSEVVD FSVPFIETGI SVMVSRSNGT VSPSAFLEPF SADVWV MMF VMLLIVSAVA VFVFEYFSPV GYNRCLADGR EPGGPSFTIG KAIWLLWGLV FNNSVPVQNP KGTTSKIMVS VWAFFAV IF LASYTANLAA FMIQEEYVDQ VSGLSDKKFQ RPNDFSPPFR FGTVPNGSTE RNIRNNYAEM HAYMGKFNQR GVDDALLS L KTGKLDAFIY DAAVLNYMAG RDEGCKLVTI GSGKVFASTG YGIAIQKDSG WKRQVDLAIL QLFGDGEMEE LEALWLTGI CHNEKNEVMS SQLDIDNMAG VFYMLGAAMA LSLITFICEH LFYWQFRHCF MGVCSGKPGM VFSISRGIYS CIHGVAIEER QSVMNSPTA TMNNTHSNIL RLLRTAKNMA NLSGVNGSPQ SALDFIRRES SVYDISEHRR SFTHSDCKSY NNPPCEENLF S DYISEVER TFGNLQLKDS NVYQDHYHHH HRPHSIGSTS SIDGLYDCDN PPFTTQPRSI SKKPLDIGLP SSKHSQLSDL YG KFSFKSD RYSGHDDLIR SDVSDISTHT VTYGNIEGNA AKRRKQQYKD SLKKRPASAK SRREFDEIEL AYRRRPPRSP DHK RYFRDK EGLRDFYLDQ FRTKENSPHW EHVDLTDIYK ERSDDFKRDS VSGGGPCTNR SHLKHGTGDK HGVVGGVPAP WEKN LTNVD WEDRSGGNFC RSCPSKLHNY SSTVAGQNSG RQACIRCEAC KKAGNLYDIS EDNSLQELDQ PAAPVAVSSN ASTTK YPQS PTNSKAQKKN RNKLRRQHSY DTFVDLQKEE AALAPRSVSL KDKGRFMDGS PYAHMFEMPA GESSFANKSS VTTAGH HHN NPGSGYMLSK SLYPDRVTQN PFIPTFGDDQ CLLHGSKSYF FRQPTVAGAS KTRPDFRALV TNKPVVSALH GAVPGRF QK DICIGNQSNP CVPNNKNPRA FNGSSNGHVY EKLSSIESDV

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.05 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9851 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model from 2D class average
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 163121
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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