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- EMDB-24468: Cryo-EM structure of apo-state of human CNGA3/CNGB3 channel -

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Basic information

Entry
Database: EMDB / ID: EMD-24468
TitleCryo-EM structure of apo-state of human CNGA3/CNGB3 channel
Map data
Sample
  • Complex: native human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3
    • Protein or peptide: Cyclic nucleotide-gated cation channel alpha-3
    • Protein or peptide: Cyclic nucleotide-gated cation channel beta-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
Keywordscone / CNG channel / cGMP / TRANSPORT PROTEIN
Function / homology
Function and homology information


inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / axon initial segment / sodium channel activity / myosin binding / monoatomic cation transmembrane transport / response to magnesium ion / monoatomic cation transport ...inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / axon initial segment / sodium channel activity / myosin binding / monoatomic cation transmembrane transport / response to magnesium ion / monoatomic cation transport / glial cell projection / cGMP binding / ligand-gated monoatomic ion channel activity / photoreceptor outer segment / transmembrane transporter complex / response to cAMP / visual perception / calcium channel activity / perikaryon / cadherin binding / dendrite / protein-containing complex binding / signal transduction / plasma membrane
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Cyclic nucleotide-gated channel alpha-3 / Cyclic nucleotide-gated channel beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZheng X / Yang J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM085234 United States
National Institutes of Health/National Eye Institute (NIH/NEI)RO1EY027800 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structure of the human cone photoreceptor cyclic nucleotide-gated channel.
Authors: Xiangdong Zheng / Zhengshan Hu / Huan Li / Jian Yang /
Abstract: Cyclic nucleotide-gated (CNG) channels transduce light-induced chemical signals into electrical signals in retinal cone and rod photoreceptors. Structures of native CNG channels, which are ...Cyclic nucleotide-gated (CNG) channels transduce light-induced chemical signals into electrical signals in retinal cone and rod photoreceptors. Structures of native CNG channels, which are heterotetramers formed by CNGA and CNGB subunits, have not been obtained. In the present study, we report a high-resolution cryo-electron microscopy structure of the human cone CNG channel in the apo closed state. The channel contains three CNGA3 and one CNGB3 subunits. Arg403 in the pore helix of CNGB3 projects into an asymmetric selectivity filter and forms hydrogen bonds with two pore-lining backbone carbonyl oxygens. Arg442 in S6 of CNGB3 protrudes into and occludes the pore below the hydrophobic cavity gate previously observed in homotetrameric CNGA channels. It is interesting that Arg403Gln is a disease mutation, and Arg442 is replaced by glutamine in some animal species with dichromatic or monochromatic vision. These and other unique structural features and the disease link conferred by CNGB3 indicate a critical role of CNGB3 in shaping cone photoresponses.
History
DepositionJul 18, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rhs
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24468.png

Downloads & links

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Map

FileDownload / File: emd_24468.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.892 Å		0.82 Å/pix.
x 360 pix.
= 296.892 Å		0.82 Å/pix.
x 360 pix.
= 296.892 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8247 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.6200932 - 2.7710898
Average (Standard dev.)0.001529973 (±0.06973086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.892 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.82470.82470.8247
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z296.892296.892296.892
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.6202.7710.002

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Supplemental data

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Sample components

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Entire : native human cone photoreceptor heterotetrameric CNG channel CNGA...

EntireName: native human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3
Components
  • Complex: native human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3
    • Protein or peptide: Cyclic nucleotide-gated cation channel alpha-3
    • Protein or peptide: Cyclic nucleotide-gated cation channel beta-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION

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Supramolecule #1: native human cone photoreceptor heterotetrameric CNG channel CNGA...

SupramoleculeName: native human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cyclic nucleotide-gated cation channel alpha-3

MacromoleculeName: Cyclic nucleotide-gated cation channel alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.233195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSMAKINT QYSHPSRTHL KVKTSDRDLN RAENGLSRAH SSSEETSSVL QPGIAMETRG LADSGQGSFT GQGIARLSRL IFLLRRWAA RHVHHQDQGP DSFPDRFRGA ELKEVSSQES NAQANVGSQE PADRGRSAWP LAKCNTNTSN NTEEEKKTKK K DAIVVDPS ...String:
GPGSMAKINT QYSHPSRTHL KVKTSDRDLN RAENGLSRAH SSSEETSSVL QPGIAMETRG LADSGQGSFT GQGIARLSRL IFLLRRWAA RHVHHQDQGP DSFPDRFRGA ELKEVSSQES NAQANVGSQE PADRGRSAWP LAKCNTNTSN NTEEEKKTKK K DAIVVDPS SNLYYRWLTA IALPVFYNWY LLICRACFDE LQSEYLMLWL VLDYSADVLY VLDVLVRART GFLEQGLMVS DT NRLWQHY KTTTQFKLDV LSLVPTDLAY LKVGTNYPEV RFNRLLKFSR LFEFFDRTET RTNYPNMFRI GNLVLYILII IHW NACIYF AISKFIGFGT DSWVYPNISI PEHGRLSRKY IYSLYWSTLT LTTIGETPPP VKDEEYLFVV VDFLVGVLIF ATIV GNVGS MISNMNASRA EFQAKIDSIK QYMQFRKVTK DLETRVIRWF DYLWANKKTV DEKEVLKSLP DKLKAEIAIN VHLDT LKKV RIFQDCEAGL LVELVLKLRP TVFSPGDYIC KKGDIGKEMY IINEGKLAVV ADDGVTQFVV LSDGSYFGEI SILNIK GSK SGNRRTANIR SIGYSDLFCL SKDDLMEALT EYPEAKKALE EKGRQILMKD NLIDEELARA GADPKDLEEK VEQLGSS LD TLQTRFARLL AEYNATQMKM KQRLSQLESQ VKGGGDKPLA DGEVPGDATK TEDKQQDYKD DDDK

UniProtKB: Cyclic nucleotide-gated channel alpha-3

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Macromolecule #2: Cyclic nucleotide-gated cation channel beta-3

MacromoleculeName: Cyclic nucleotide-gated cation channel beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.450758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSFKSLTKV NKVKPIGENN ENEQSSRRNE EGSHPSNQSQ QTTAQEENKG EEKSLKTKS TPVTSEEPHT NIQDKLSKKN SSGDLTTNPD PQNAAEPTGT VPEQKEMDPG KEGPNSPQNK PPAAPVINEY A DAQLHNLV ...String:
MGSWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSFKSLTKV NKVKPIGENN ENEQSSRRNE EGSHPSNQSQ QTTAQEENKG EEKSLKTKS TPVTSEEPHT NIQDKLSKKN SSGDLTTNPD PQNAAEPTGT VPEQKEMDPG KEGPNSPQNK PPAAPVINEY A DAQLHNLV KRMRQRTALY KKKLVEGDLS SPEASPQTAK PTAVPPVKES DDKPTEHYYR LLWFKVKKMP LTEYLKRIKL PN SIDSYTD RLYLLWLLLV TLAYNWNCCF IPLRLVFPYQ TADNIHYWLI ADIICDIIYL YDMLFIQPRL QFVRGGDIIV DSN ELRKHY RTSTKFQLDV ASIIPFDICY LFFGFNPMFR ANRMLKYTSF FEFNHHLESI MDKAYIYRVI RTTGYLLFIL HINA CVYYW ASNYEGIGTT RWVYDGEGNE YLRCYYWAVR TLITIGGLPE PQTLFEIVFQ LLNFFSGVFV FSSLIGQMRD VIGAA TANQ NYFRACMDDT IAYMNNYSIP KLVQKRVRTW YEYTWDSQRM LDESDLLKTL PTTVQLALAI DVNFSIISKV DLFKGC DTQ MIYDMLLRLK SVLYLPGDFV CKKGEIGKEM YIIKHGEVQV LGGPDGTKVL VTLKAGSVFG EISLLAAGGG NRRTANV VA HGFANLLTLD KKTLQEILVH YPDSERILMK KARVLLKQKA KTAEATPPRK DLALLFPPKE ETPKLFKTLL GGTGKASL A RLLKLKREQA AQKKENSEGG EEEGKENEDK QKENEDKQKE NEDKGKENED KDKGREPEEK PLDRPECTAS PIAVEEEPH SVRRTVLPRG TSRQSLIISM APSAEGGEEV LTIEVKEKAK Q

UniProtKB: Cyclic nucleotide-gated channel beta-3

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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

Concentration1.5 mg/mL
BufferpH: 8.58
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 57.63 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wej

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 205492
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: RELION

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