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- EMDB-12805: Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12805 | |||||||||
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Title | Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD) | |||||||||
![]() | Composite map generated based on masked refinement maps of LBD and TMD. | |||||||||
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![]() | AMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / axonal spine / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / localization within membrane / COPII-mediated vesicle transport ...negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / axonal spine / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / localization within membrane / COPII-mediated vesicle transport / cellular response to ammonium ion / response to sucrose / L-type voltage-gated calcium channel complex / postsynaptic neurotransmitter receptor diffusion trapping / neuron spine / myosin V binding / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / regulation of monoatomic ion transmembrane transport / LGI-ADAM interactions / proximal dendrite / protein phosphatase 2B binding / cellular response to L-glutamate / response to arsenic-containing substance / regulation of NMDA receptor activity / cellular response to dsRNA / dendritic spine membrane / long-term synaptic depression / Synaptic adhesion-like molecules / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / response to morphine / neuronal cell body membrane / spine synapse / dendritic spine neck / protein kinase A binding / dendritic spine head / peptide hormone receptor binding / cellular response to amine stimulus / response to psychosocial stress / spinal cord development / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / transmission of nerve impulse / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / behavioral response to pain / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / adenylate cyclase binding / ionotropic glutamate receptor complex / immunoglobulin binding / asymmetric synapse / conditioned place preference / excitatory synapse / response to electrical stimulus / regulation of receptor recycling / G-protein alpha-subunit binding / positive regulation of excitatory postsynaptic potential / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / positive regulation of synaptic transmission / postsynaptic density, intracellular component / regulation of postsynaptic membrane neurotransmitter receptor levels / neuronal action potential / voltage-gated calcium channel activity / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / synapse assembly / vesicle-mediated transport / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / SNARE binding / dendritic shaft / regulation of membrane potential / response to nutrient levels / calcium channel regulator activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / cellular response to amino acid stimulus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Zhang D / Watson JF / Matthews PM / Cais O / Greger IH | |||||||||
Funding support | 2 items
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![]() | ![]() Title: Gating and modulation of a hetero-octameric AMPA glutamate receptor. Authors: Danyang Zhang / Jake F Watson / Peter M Matthews / Ondrej Cais / Ingo H Greger / ![]() ![]() Abstract: AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning. A diverse array of AMPAR signalling complexes are ...AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1-GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28 KB 28 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() ![]() | 11.3 KB 11.4 KB 11.3 KB | Display Display Display | ![]() |
Images | ![]() | 202.9 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() ![]() ![]() | 11 MB 1.4 MB 8.8 MB 7.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 409 KB | Display | ![]() |
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Full document | ![]() | 408.6 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oceMC ![]() 7ocaC ![]() 7occC ![]() 7ocdC ![]() 7ocfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Composite map generated based on masked refinement maps of LBD and TMD. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Masked refinement map focusing on TMD
File | emd_12805_additional_1.map | ||||||||||||
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Annotation | Masked refinement map focusing on TMD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Masked refinement map focusing on CNIH2
File | emd_12805_additional_2.map | ||||||||||||
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Annotation | Masked refinement map focusing on CNIH2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Masked refinement map focusing on LBD
File | emd_12805_additional_3.map | ||||||||||||
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Annotation | Masked refinement map focusing on LBD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: EMDA best map generated based on masked refinement...
File | emd_12805_additional_4.map | ||||||||||||
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Annotation | EMDA best map generated based on masked refinement maps of LBD and TMD. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : GluA1/A2 heterotetramer in complex with auxiliary subunits TARP g...
Entire | Name: GluA1/A2 heterotetramer in complex with auxiliary subunits TARP gamma 8 and CNIH2 |
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Components |
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-Supramolecule #1: GluA1/A2 heterotetramer in complex with auxiliary subunits TARP g...
Supramolecule | Name: GluA1/A2 heterotetramer in complex with auxiliary subunits TARP gamma 8 and CNIH2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 527 KDa |
-Macromolecule #1: Glutamate receptor 1
Macromolecule | Name: Glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 102.66193 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR ...String: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR VLDTAAEKNW QVTAVNILTT TEEGYRMLFQ DLEKKKERLV VVDCESERLN AILGQIVKLE KNGIGYHYIL AN LGFMDID LNKFKESGAN VTGFQLVNYT DTIPARIMQQ WRTSDSRDHT RVDWKRPKYT SALTYDGVKV MAEAFQSLRR QRI DISRRG NAGDCLANPA VPWGQGIDIQ RALQQVRFEG LTGNVQFNEK GRRTNYTLHV IEMKHDGIRK IGYWNEDDKF VPAA TDAQA GGDNSSVQNR TYIVTTILED PYVMLKKNAN QFEGNDRYEG YCVELAAEIA KHVGYSYRLE IVSDGKYGAR DPDTK AWNG MVGELVYGRA DVAVAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HSEEFEEGRD QTTSDQSNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL EAGSTKEFFR RSKIAVFEKM WTYMKSAEPS VFVRTTEEGM IRVRKSKG K YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SALRGPVNLA VLKLSEQGVL DKLKSKWWYD KGECGSKDS GSKDKTSALS LSNVAGVFYI LIGGLGLAML VALIEFCYKS RSESKRMKGF CLIPQQSINE AIRTSTLPRN SGAGASGGGG SGENGRVVS QDFPKSMQSI PCMSHSSGMP LGATGL UniProtKB: Glutamate receptor 1 |
-Macromolecule #2: Glutamate receptor 2
Macromolecule | Name: Glutamate receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 96.247055 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA ...String: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA AEKKWQVTAI NVGNINNDKK DETYRSLFQD LELKKERRVI LDCERDKVND IVDQVITIGK HVKGYHYIIA NL GFTDGDL LKIQFGGANV SGFQIVDYDD SLVSKFIERW STLEEKEYPG AHTATIKYTS ALTYDAVQVM TEAFRNLRKQ RIE ISRRGN AGDCLANPAV PWGQGVEIER ALKQVQVEGL SGNIKFDQNG KRINYTINIM ELKTNGPRKI GYWSEVDKMV VTLT ELPSG NDTSGLENKT VVVTTILESP YVMMKKNHEM LEGNERYEGY CVDLAAEIAK HCGFKYKLTI VGDGKYGARD ADTKI WNGM VGELVYGKAD IAIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVV LFL VSRFSPYEWH TEEFEDGRET QSSESTNEFG IFNSLWFSLG AFMRQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTAN LA AFLTVERMVS PIESAEDLSK QTEIAYGTLD SGSTKEFFRR SKIAVFDKMW TYMRSAEPSV FVRTTAEGVA RVRKSKGK Y AYLLESTMNE YIEQRKPCDT MKVGGNLDSK GYGIATPKGS SLGTPVNLAV LKLSEQGVLD KLKNKWWYDK GECGAKDSG SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS UniProtKB: Glutamate receptor 2 |
-Macromolecule #3: Protein cornichon homolog 2
Macromolecule | Name: Protein cornichon homolog 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.000605 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAFTFAAFCY MLTLVLCASL IFFVIWHIIA FDELRTDFKN PIDQGNPARA RERLKNIERI CCLLRKLVVP EYSIHGLFCL MFLCAAEWV TLGLNIPLLF YHLWRYFHRP ADGSEVMYDA VSIMNADILN YCQKESWCKL AFYLLSFFYY LYSMVYTLVS F ENLYFQSG GSTETSQVAP AYPYDVPDYA UniProtKB: Protein cornichon homolog 2 |
-Macromolecule #4: Voltage-dependent calcium channel gamma-8 subunit
Macromolecule | Name: Voltage-dependent calcium channel gamma-8 subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.518957 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ESLKRWNEER GLWCEKGVQV LLTTIGAFAA FGLMTIAIST DYWLYTRALI CNTTNLTAGD DGPPHRGGSG SSEKKDPGGL THSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG A GILFVAAG ...String: ESLKRWNEER GLWCEKGVQV LLTTIGAFAA FGLMTIAIST DYWLYTRALI CNTTNLTAGD DGPPHRGGSG SSEKKDPGGL THSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG A GILFVAAG LSNIIGVIVY ISANAGEPGP KRDEEKKNHY SYGWSFYFGG LSFILAEVIG VLAVNIYIER SREAHCQSRS DL LKAGGGA GGSGGSGPSA ILRLPSYRFR YRRRSRSSSR GSSEASPSRD ASPGGPGGPG FASTDISMYT LSRDPSKGSV AAG LASAGG GGGGAGVGAY GGAAGAAGGG GTGSERDRGS SAGFLTLHNA FPKEAASGVT VTVTGPPAAP APAPPAPAAP APGT LSKEA AASNTNTLNR KLEVLFQ UniProtKB: Voltage-dependent calcium channel gamma-8 subunit |
-Macromolecule #5: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-s...
Macromolecule | Name: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide type: ligand / ID: 5 / Number of copies: 4 / Formula: E2Q |
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Molecular weight | Theoretical: 336.28 Da |
Chemical component information | ![]() ChemComp-E2Q: |
-Macromolecule #6: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 46 / Formula: PC1 |
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Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ![]() ChemComp-PC1: |
-Macromolecule #7: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 2 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Purified protein was incubated with 100 uM NBQX for at least 30 min on ice before freezing |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 113 | ||||||
Output model | ![]() PDB-7oce: |