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- EMDB-4575: Full length GluA1/2-gamma8 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4575
TitleFull length GluA1/2-gamma8 complex
Map data
Sample
  • Complex: GluA1/A2 bound to gamma-8
    • Protein or peptide: GluA1
    • Protein or peptide: Glutamate receptor 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-8 subunit
  • Ligand: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAMPAR / ion channel / GluA1 / GluA2 / tarp / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / COPII-mediated vesicle transport / cellular response to ammonium ion / response to sucrose / L-type voltage-gated calcium channel complex ...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 / COPII-mediated vesicle transport / cellular response to ammonium ion / response to sucrose / L-type voltage-gated calcium channel complex / myosin V binding / neuron spine / postsynaptic neurotransmitter receptor diffusion trapping / proximal dendrite / LGI-ADAM interactions / protein phosphatase 2B binding / Trafficking of AMPA receptors / regulation of AMPA receptor activity / response to arsenic-containing substance / regulation of monoatomic ion transmembrane transport / channel regulator activity / ligand-gated calcium channel activity / cellular response to L-glutamate / cellular response to dsRNA / dendritic spine membrane / beta-2 adrenergic receptor binding / long-term synaptic depression / Synaptic adhesion-like molecules / cellular response to peptide hormone stimulus / spine synapse / dendritic spine cytoplasm / dendritic spine neck / cellular response to amine stimulus / dendritic spine head / response to psychosocial stress / peptide hormone receptor binding / response to morphine / neuronal cell body membrane / spinal cord development / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / protein kinase A binding / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / response to lithium ion / transmission of nerve impulse / AMPA glutamate receptor clustering / behavioral response to pain / kainate selective glutamate receptor activity / immunoglobulin binding / adenylate cyclase binding / asymmetric synapse / AMPA glutamate receptor complex / response to electrical stimulus / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / conditioned place preference / glutamate receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / long-term memory / voltage-gated calcium channel activity / postsynaptic density, intracellular component / response to fungicide / neuronal action potential / regulation of synaptic transmission, glutamatergic / positive regulation of synaptic transmission, glutamatergic / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / cytoskeletal protein binding / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / synapse assembly / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / positive regulation of excitatory postsynaptic potential / dendritic shaft / synaptic membrane / SNARE binding / PDZ domain binding / response to cocaine / neuromuscular junction / calcium channel regulator activity / synaptic transmission, glutamatergic / cellular response to amino acid stimulus / establishment of protein localization / protein tetramerization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
Similarity search - Function
Voltage-dependent calcium channel, gamma-8 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...Voltage-dependent calcium channel, gamma-8 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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 1 / Glutamate receptor 2 / Voltage-dependent calcium channel gamma-8 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsHerguedas B / Garcia-Nafria J
CitationJournal: Science / Year: 2019
Title: Architecture of the heteromeric GluA1/2 AMPA receptor in complex with the auxiliary subunit TARP γ8.
Authors: Beatriz Herguedas / Jake F Watson / Hinze Ho / Ondrej Cais / Javier García-Nafría / Ingo H Greger /
Abstract: AMPA-type glutamate receptors (AMPARs) mediate excitatory neurotransmission and are central regulators of synaptic plasticity, a molecular mechanism underlying learning and memory. Although AMPARs ...AMPA-type glutamate receptors (AMPARs) mediate excitatory neurotransmission and are central regulators of synaptic plasticity, a molecular mechanism underlying learning and memory. Although AMPARs act predominantly as heteromers, structural studies have focused on homomeric assemblies. Here, we present a cryo-electron microscopy structure of the heteromeric GluA1/2 receptor associated with two transmembrane AMPAR regulatory protein (TARP) γ8 auxiliary subunits, the principal AMPAR complex at hippocampal synapses. Within the receptor, the core subunits arrange to give the GluA2 subunit dominant control of gating. This structure reveals the geometry of the Q/R site that controls calcium flux, suggests association of TARP-stabilized lipids, and demonstrates that the extracellular loop of γ8 modulates gating by selectively interacting with the GluA2 ligand-binding domain. Collectively, this structure provides a blueprint for deciphering the signal transduction mechanisms of synaptic AMPARs.
History
DepositionJan 30, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qkz
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4575.png

Downloads & links

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Map

FileDownload / File: emd_4575.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 220 pix.
= 308. Å		1.4 Å/pix.
x 220 pix.
= 308. Å		1.4 Å/pix.
x 220 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.057344325 - 0.08786715
Average (Standard dev.)0.0005879226 (±0.0033054699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z308.000308.000308.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0570.0880.001

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Supplemental data

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Sample components

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Entire : GluA1/A2 bound to gamma-8

EntireName: GluA1/A2 bound to gamma-8
Components
  • Complex: GluA1/A2 bound to gamma-8
    • Protein or peptide: GluA1
    • Protein or peptide: Glutamate receptor 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-8 subunit
  • Ligand: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GluA1/A2 bound to gamma-8

SupramoleculeName: GluA1/A2 bound to gamma-8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 447 kDa/nm

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Macromolecule #1: GluA1

MacromoleculeName: GluA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 100.739602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADYKDDDDKN FPNNIQIGGL FPNQQSQEHA AFRFALSQLT EPPKLLPQID IVNISDSFEM TYRFCSQFSK GVYAIFGFYE RRTVNMLTS FCGALHVCFI TPSFPVDTSN QFVLQLRPEL QEALISIIDH YKWQTFVYIY DADRGLSVLQ RVLDTAAEKN W QVTAVNIL ...String:
ADYKDDDDKN FPNNIQIGGL FPNQQSQEHA AFRFALSQLT EPPKLLPQID IVNISDSFEM TYRFCSQFSK GVYAIFGFYE RRTVNMLTS FCGALHVCFI TPSFPVDTSN QFVLQLRPEL QEALISIIDH YKWQTFVYIY DADRGLSVLQ RVLDTAAEKN W QVTAVNIL TTTEEGYRML FQDLEKKKER LVVVDCESER LNAILGQIVK LEKNGIGYHY ILANLGFMDI DLNKFKESGA NV TGFQLVN YTDTIPARIM QQWRTSDSRD HTRVDWKRPK YTSALTYDGV KVMAEAFQSL RRQRIDISRR GNAGDCLANP AVP WGQGID IQRALQQVRF EGLTGNVQFN EKGRRTNYTL HVIEMKHDGI RKIGYWNEDD KFVPAATDAQ AGGDNSSVQN RTYI VTTIL EDPYVMLKKN ANQFEGNDRY EGYCVELAAE IAKHVGYSYR LEIVSDGKYG ARDPDTKAWN GMVGELVYGR ADVAV APLT ITLVREEVID FSKPFMSLGI SIMIKKPQKS KPGVFSFLDP LAYEIWMCIV FAYIGVSVVL FLVSRFSPYE WHSEEF EEG RDQTTSDQSN EFGIFNSLWF SLGAFMQQGC DISPRSLSGR IVGGVWWFFT LIIISSYTAN LAAFLTVERM VSPIESA ED LAKQTEIAYG TLEAGSTKEF FRRSKIAVFE KMWTYMKSAE PSVFVRTTEE GMIRVRKSKG KYAYLLESTM NEYIEQRK P CDTMKVGGNL DSKGYGIATP KGSALRGPVN LAVLKLSEQG VLDKLKSKWW YDKGECGSKD SGSKDKTSAL SLSNVAGVF YILIGGLGLA MLVALIEFCY KSRSESKRMK GFCLIPQQSI NEAIRTSTLP RNSGAGASGG GGSGENGRVV SQDFPKSMQS IPCMSHSSG MPLGATGL

UniProtKB: Glutamate receptor 1

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Macromolecule #2: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 93.880078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VSSNSIQIGG LFPRGADQEY SAFRVGMVQF STSEFRLTPH IDNLEVANSF AVTNAFCSQF SRGVYAIFGF YDKKSVNTIT SFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE KKWQVTAINV G NINNDKKD ...String:
VSSNSIQIGG LFPRGADQEY SAFRVGMVQF STSEFRLTPH IDNLEVANSF AVTNAFCSQF SRGVYAIFGF YDKKSVNTIT SFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE KKWQVTAINV G NINNDKKD ETYRSLFQDL ELKKERRVIL DCERDKVNDI VDQVITIGKH VKGYHYIIAN LGFTDGDLLK IQFGGANVSG FQ IVDYDDS LVSKFIERWS TLEEKEYPGA HTATIKYTSA LTYDAVQVMT EAFRNLRKQR IEISRRGNAG DCLANPAVPW GQG VEIERA LKQVQVEGLS GNIKFDQNGK RINYTINIME LKTNGPRKIG YWSEVDKMVV TLTELPSGND TSGLENKTVV VTTI LESPY VMMKKNHEML EGNERYEGYC VDLAAEIAKH CGFKYKLTIV GDGKYGARDA DTKIWNGMVG ELVYGKADIA IAPLT ITLV REEVIDFSKP FMSLGISIMI KKPQKSKPGV FSFLDPLAYE IWMCIVFAYI GVSVVLFLVS RFSPYEWHTE EFEDGR ETQ SSESTNEFGI FNSLWFSLGA FMRQGCDISP RSLSGRIVGG VWWFFTLIII SSYTANLAAF LTVERMVSPI ESAEDLS KQ TEIAYGTLDS GSTKEFFRRS KIAVFDKMWT YMRSAEPSVF VRTTAEGVAR VRKSKGKYAY LLESTMNEYI EQRKPCDT M KVGGNLDSKG YGIATPKGSS LGTPVNLAVL KLSEQGVLDK LKNKWWYDKG ECGAKDSGSK EKTSALSLSN VAGVFYILV GGLGLAMLVA LIEFCYKSRA EAKRMKVAKN PQNINPSSS

UniProtKB: Glutamate receptor 2

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Macromolecule #3: Voltage-dependent calcium channel gamma-8 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-8 subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.592008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRI CCLEGLKRGV CVKINHFPED TDYDHDSSEY LLRVVRASSI FPILSAILLL LGGVCVAASR VYKSKRNIIL G AGILFVAA ...String:
GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRI CCLEGLKRGV CVKINHFPED TDYDHDSSEY LLRVVRASSI FPILSAILLL LGGVCVAASR VYKSKRNIIL G AGILFVAA GLSNIIGVIV YISANAGEPG PKRDEEKKNH YSYGWSFYFG GLSFILAEVI GVLAVNIYIE RSREAHCQSR SD LLKAGGG AGGSGGSGPS AILRLPSYRF RYRRRSRSSS RGSSEASPSR DASPGGPGGP GFASTDISMY TLSRDPSKGS VAA GLASAG GGGGGAGVGA YGGAAGAAGG GGTGSERDRG SSAGFLTLHN AFPKEAASGV TVTVTGPPAA PAPAPPAPAA PAPG TLSKE AAASNTNTLN RKLEVLFQ

UniProtKB: Voltage-dependent calcium channel gamma-8 subunit

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Macromolecule #6: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-s...

MacromoleculeName: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
type: ligand / ID: 6 / Number of copies: 4 / Formula: E2Q
Molecular weightTheoretical: 336.28 Da
Chemical component information

ChemComp-E2Q:
6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide / antagonist*YM

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / 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

Concentration0.4 mg/mL
BufferpH: 8
Details: 25 mM TRIS, pH 8, 150 mM NaCl and 0.1 % digitonin (w/v)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3uL on grid, 60 sec incubation and 4sec blotting time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K / Max: 100.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 3 / Number real images: 5005 / Average exposure time: 14.0 sec. / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.9 µm / Nominal defocus min: -0.2 µm / Nominal magnification: 105000
Sample stageSpecimen 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

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: ab initio model generated with RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 183881
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6qkc

source_name: PDB, initial_model_type: experimental model

3saj

source_name: PDB, initial_model_type: experimental model

3h5v

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6qkz:
Full length GluA1/2-gamma8 complex

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