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Yorodumi- EMDB-36209: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36209 | |||||||||
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Title | Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | membrane protein / ion channel | |||||||||
Function / homology | Function and homology information neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / negative regulation of dendritic spine development / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / negative regulation of dendritic spine development / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / serotonin metabolic process / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / sleep / voltage-gated monoatomic cation channel activity / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / locomotion / regulation of monoatomic cation transmembrane transport / response to morphine / cellular response to lipid / glutamate receptor activity / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / regulation of NMDA receptor activity / protein heterotetramerization / glutamate binding / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of axonogenesis / spinal cord development / dopamine metabolic process / suckling behavior / startle response / monoatomic cation transmembrane transport / dendrite development / regulation of neuronal synaptic plasticity / response to amine / modulation of excitatory postsynaptic potential / response to lithium ion / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / cellular response to glycine / positive regulation of dendritic spine maintenance / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of protein targeting to membrane / regulation of postsynaptic membrane potential / phosphatase binding / glutamate receptor binding / postsynaptic density, intracellular component / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / multicellular organismal response to stress / long-term memory / monoatomic cation channel activity / regulation of neuron apoptotic process / presynaptic active zone membrane / synaptic cleft / glutamate-gated receptor activity / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Muromegalovirus G4 / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.73 Å | |||||||||
Authors | Kou Z / Zhu S | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Probing the architecture of native GluN1-N2-N3A NMDA receptors by cryo-EM and click chemistry. Authors: Kou Z / Zhu S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36209.map.gz | 227.6 MB | EMDB map data format | |
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Header (meta data) | emd-36209-v30.xml emd-36209.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36209_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_36209.png | 36 KB | ||
Filedesc metadata | emd-36209.cif.gz | 7.9 KB | ||
Others | emd_36209_half_map_1.map.gz emd_36209_half_map_2.map.gz | 193.8 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36209 | HTTPS FTP |
-Related structure data
Related structure data | 8jf7MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36209.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36209_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36209_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with ...
Entire | Name: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab |
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Components |
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-Supramolecule #1: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with ...
Supramolecule | Name: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4-#5, #1-#3, #7, #6 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Macromolecule #1: Glutamate receptor ionotropic, NMDA 1
Macromolecule | Name: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 95.372164 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 MEARELEARV 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 YGFCIDLLIK 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 KDARRKQ UniProtKB: Glutamate receptor ionotropic, NMDA 1 |
-Macromolecule #2: Glutamate receptor ionotropic, NMDA 2A,Enhanced green fluorescent...
Macromolecule | Name: Glutamate receptor ionotropic, NMDA 2A,Enhanced green fluorescent protein type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Muromegalovirus G4 |
Molecular weight | Theoretical: 125.325992 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGRLGYWTLL VLPALLVWRD PAQNAAAEKG PPALNIAVLL GHSHDVTERE LRNLWGPEQA TGLPLDVNVV ALLMNRTDPK SLITHVCDL MSGARIHGLV FGDDTDQEAV AQMLDFISSQ TFIPILGIHG GASMIMADKD PTSTFFQFGA SIQQQATVML K IMQDYDWH ...String: MGRLGYWTLL VLPALLVWRD PAQNAAAEKG PPALNIAVLL GHSHDVTERE LRNLWGPEQA TGLPLDVNVV ALLMNRTDPK SLITHVCDL MSGARIHGLV FGDDTDQEAV AQMLDFISSQ TFIPILGIHG GASMIMADKD PTSTFFQFGA SIQQQATVML K IMQDYDWH VFSLVTTIFP GYRDFISFIK TTVDNSFVGW DMQNVITLDT SFEDAKTQVQ LKKIHSSVIL LYCSKDEAVL IL SEARSLG LTGYDFFWIV PSLVSGNTEL IPKEFPSGLI SVSYDDWDYS LEARVRDGLG ILTTAASSML EKFSYIPEAK ASC YGQAEK PETPLHTLHQ FMVNVTWDGK DLSFTEEGYQ VHPRLVVIVL NKDREWEKVG KWENQTLSLR HAVWPRYKSF SDCE PDDNH LSIVTLEEAP FVIVEDIDPL TETCVRNTVP CRKFVKINNS TNEGMNVKKC CKGFCIDILK KLSRTVKFTY DLYLV TNGK HGKKVNNVWN GMIGEVVYQR AVMAVGSLTI NEERSEVVDF SVPFVETGIS VMVSRSNGTV SPSAFLEPFS ASVWVM MFV MLLIVSAIAV FVFEYFSPVG YNRNLAKGKA PHGPSFTIGK AIWLLWGLVF NNSVPVQNPK GTTSKIMVSV WAFFAVI FL ASYTANLAAF MIQEEFVDQV TGLSDKKFQR PHDYSPPFRF GTVPNGSTER NIRNNYPYMH QYMTRFNQRG VEDALVSL K TGKLDAFIYD AAVLNYKAGR DEGCKLVTIG SGYIFASTGY GIALQKGSPW KRQIDLALLQ FVGDGEMEEL ETLWLTGIC HNEKNEVMSS QLDIDNMAGV FYMLAAAMAL SLITFIWEHL FYKSRAEAKR MKGLEVLFQG PAAAAVSKGE ELFTGVVPIL VELDGDVNG HKFSVSGEGE GDATYGKLTL KFICTTGKLP VPWPTLVTTL TYGVQCFSRY PDHMKQHDFF KSAMPEGYVQ E RTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NYNSHNVYIM ADKQKNGIKV NFKIRHNIED GS VQLADHY QQNTPIGDGP VLLPDNHYLS TQSKLSKDPN EKRDHMVLLE FVTAAGITLG MDELYKSGLR SHHHHHHHH UniProtKB: Glutamate receptor ionotropic, NMDA 2A, Enhanced green fluorescent protein |
-Macromolecule #3: Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent...
Macromolecule | Name: Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent protein type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Muromegalovirus G4 |
Molecular weight | Theoretical: 137.362844 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MRRLSLWWLL SRVCLLLPPP CALVLAGVPS SSSHPQPCQI LKRIGHAVRV GAVHLQPWTT APRAASRAQE GGRAGAQRDD PESGTWRPP APSQGARWLG SALHGRGPPG SRKLGEGAGA ETLWPRDALL FAVENLNRVE GLLPYNLSLE VVMAIEAGLG D LPLMPFSS ...String: MRRLSLWWLL SRVCLLLPPP CALVLAGVPS SSSHPQPCQI LKRIGHAVRV GAVHLQPWTT APRAASRAQE GGRAGAQRDD PESGTWRPP APSQGARWLG SALHGRGPPG SRKLGEGAGA ETLWPRDALL FAVENLNRVE GLLPYNLSLE VVMAIEAGLG D LPLMPFSS PSSPWSSDPF SFLQSVCHTV VVQGVSALLA FPQSQGEMME LDLVSSVLHI PVLSIVRHEF PRESQNPLHL QL SLENSLS SDADVTVSIL TMNNWYNFSL LLCQEDWNIT DFLLLTENNS KFHLESVINI TANLSSTKDL LSFLQVQMDN IRN STPTMV MFGCDMDSIR QIFEMSTQFG LSPPELHWVL GDSQNVEELR TEGLPLGLIA HGKTTQSVFE YYVQDAMELV ARAV ATATM IQPELALLPS TMNCMDVKTT NLTSGQYLSR FLANTTFRGL SGSIKVKGST IISSENNFFI WNLQHDPMGK PMWTR LGSW QGGRIVMDSG IWPEQAQRHK THFQHPNKLH LRVVTLIEHP FVFTREVDDE GLCPAGQLCL DPMTNDSSML DRLFSS LHS SNDTVPIKFK KCCYGYCIDL LEQLAEDMNF DFDLYIVGDG KYGAWKNGHW TGLVGDLLSG TANMAVTSFS INTARSQ VI DFTSPFFSTS LGILVRTRDT AAPIGAFMWP LHWTMWLGIF VALHITAIFL TLYEWKSPFG MTPKGRNRNK VFSFSSAL N VCYALLFGRT AAIKPPKCWT GRFLMNLWAI FCMFCLSTYT ANLAAVMVGE KIYEELSGIH DPKLHHPSQG FRFGTVRES SAEDYVRQSF PEMHEYMRRY NVPATPDGVQ YLKNDPEKLD AFIMDKALLD YEVSIDADCK LLTVGKPFAI EGYGIGLPPN SPLTSNISE LISQYKSHGF MDVLHDKWYK VVPCGKRSFA VTETLQMEIK HFSGLFVLLC IGFGLSILTT IGEHIVHRLL L PRIKNLEV LFQGPAAAAV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TT LTYGVQC FSRYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEY NYNSHN VYIMADKQKN GIKVNFKIRH NIEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSKLSK DPNEKRDHMV LLEF VTAAG ITLGMDELYK SGLRSWSHPQ FEK UniProtKB: Glutamate receptor ionotropic, NMDA 3A, Enhanced green fluorescent protein |
-Macromolecule #4: GluN1-specific antibody fragment light chain
Macromolecule | Name: GluN1-specific antibody fragment light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.739438 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQWVLLLWV PGSTGDIVLT QSPASLAVSL GQRATISCKA SQSVDYDGNS YMNWYQQKPG QPPKLLIYAA SNLESGIPAR FSGSGSGTD FTLNIHPVEE EDAATYYCQQ GNEDPPTFGG GTKLEIKRAD ARTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK ...String: DIQWVLLLWV PGSTGDIVLT QSPASLAVSL GQRATISCKA SQSVDYDGNS YMNWYQQKPG QPPKLLIYAA SNLESGIPAR FSGSGSGTD FTLNIHPVEE EDAATYYCQQ GNEDPPTFGG GTKLEIKRAD ARTVAAPSVF IFPPSDEQLK SGTASVVCLL N NFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC |
-Macromolecule #5: GluN1-specific antibody fragment heavy chain
Macromolecule | Name: GluN1-specific antibody fragment heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.432072 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNKLEWMG YISYSGSTGY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARL YYGFYGMDYW GQGTSVTVSS AKTTTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNKLEWMG YISYSGSTGY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARL YYGFYGMDYW GQGTSVTVSS AKTTTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDK |
-Macromolecule #6: GluN2A-specific antibody fragment light chain
Macromolecule | Name: GluN2A-specific antibody fragment light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.234682 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVYA TTNLADGVPS RFSGSGSGTQ YSLKINSLQS EDFGSYYCQ HFWGTPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVYA TTNLADGVPS RFSGSGSGTQ YSLKINSLQS EDFGSYYCQ HFWGTPWTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG |
-Macromolecule #7: GluN2A-specific antibody fragment heavy chain
Macromolecule | Name: GluN2A-specific antibody fragment heavy chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 24.936934 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: QVTLKESGPG ILQPSQTLSL TCSFSGFSLS SSGVGVGWIR QPSGKGLEWL AHIWWDDIKR YNPALKSRLT ISKDTSSSQV FLKIASVAT ADTATYYCTR METAWFPYWG QGTLVTVSAK RADARTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE A KVQWKVDN ...String: QVTLKESGPG ILQPSQTLSL TCSFSGFSLS SSGVGVGWIR QPSGKGLEWL AHIWWDDIKR YNPALKSRLT ISKDTSSSQV FLKIASVAT ADTATYYCTR METAWFPYWG QGTLVTVSAK RADARTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE A KVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |