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- EMDB-24845: Human KATP channel in open conformation, focused on Kir and one S... -

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Basic information

Entry
Database: EMDB / ID: EMD-24845
TitleHuman KATP channel in open conformation, focused on Kir and one SUR, position 4
Map datafocused on Kir (C166S G334D) and one SUR after sharpening (B-factor: 60.2), position4
Sample
  • Complex: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
    • Complex: Kir6.2 (C166S G334D) subunit of human KATP
      • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
    • Complex: SUR1 subunit of human KATP
      • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


negative regulation of neuroblast migration / positive regulation of uterine smooth muscle relaxation / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / potassium ion-transporting ATPase complex / positive regulation of tight junction disassembly / negative regulation of low-density lipoprotein particle clearance / negative regulation of blood-brain barrier permeability / response to resveratrol / ATP-activated inward rectifier potassium channel activity ...negative regulation of neuroblast migration / positive regulation of uterine smooth muscle relaxation / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / potassium ion-transporting ATPase complex / positive regulation of tight junction disassembly / negative regulation of low-density lipoprotein particle clearance / negative regulation of blood-brain barrier permeability / response to resveratrol / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / cell body fiber / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / positive regulation of potassium ion transport / ATPase-coupled monoatomic cation transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / response to pH / inorganic cation transmembrane transport / ankyrin binding / neuromuscular process / negative regulation of glial cell proliferation / response to ATP / response to zinc ion / action potential / potassium ion import across plasma membrane / intracellular glucose homeostasis / response to testosterone / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ATPase-coupled transmembrane transporter activity / intercalated disc / potassium channel activity / axolemma / ABC-type transporter activity / negative regulation of insulin secretion / heat shock protein binding / T-tubule / potassium ion transmembrane transport / negative regulation of angiogenesis / acrosomal vesicle / determination of adult lifespan / response to ischemia / Regulation of insulin secretion / female pregnancy / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / ADP binding / response to insulin / visual learning / potassium ion transport / transmembrane transport / sarcolemma / memory / cellular response to nicotine / synaptic vesicle membrane / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / nuclear envelope / response to estradiol / presynaptic membrane / transmembrane transporter binding / response to lipopolysaccharide / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / : ...Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin E-set / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-sensitive inward rectifier potassium channel 11 / ATP-binding cassette sub-family C member 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhao C / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Molecular structure of an open human K channel.
Authors: Chen Zhao / Roderick MacKinnon /
Abstract: K channels are metabolic sensors that translate intracellular ATP/ADP balance into membrane excitability. The molecular composition of K includes an inward-rectifier potassium channel (Kir) and an ...K channels are metabolic sensors that translate intracellular ATP/ADP balance into membrane excitability. The molecular composition of K includes an inward-rectifier potassium channel (Kir) and an ABC transporter-like sulfonylurea receptor (SUR). Although structures of K have been determined in many conformations, in all cases, the pore in Kir is closed. Here, we describe human pancreatic K (hK) structures with an open pore at 3.1- to 4.0-Å resolution using single-particle cryo-electron microscopy (cryo-EM). Pore opening is associated with coordinated structural changes within the ATP-binding site and the channel gate in Kir. Conformational changes in SUR are also observed, resulting in an area reduction of contact surfaces between SUR and Kir. We also observe that pancreatic hK exhibits the unique (among inward-rectifier channels) property of PIP-independent opening, which appears to be correlated with a docked cytoplasmic domain in the absence of PIP.
History
DepositionSep 12, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7s60
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24845.png

Downloads & links

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Map

FileDownload / File: emd_24845.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused on Kir (C166S G334D) and one SUR after sharpening (B-factor: 60.2), position4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 364 pix.
= 473.2 Å		1.3 Å/pix.
x 364 pix.
= 473.2 Å		1.3 Å/pix.
x 364 pix.
= 473.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.0810524 - 2.6417978
Average (Standard dev.)-0.0050696232 (±0.082639925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 473.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z473.200473.200473.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-1.0812.642-0.005

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Supplemental data

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Sample components

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Entire : Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1

EntireName: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
Components
  • Complex: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
    • Complex: Kir6.2 (C166S G334D) subunit of human KATP
      • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
    • Complex: SUR1 subunit of human KATP
      • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1

SupramoleculeName: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 881.87 kDa/nm

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Supramolecule #2: Kir6.2 (C166S G334D) subunit of human KATP

SupramoleculeName: Kir6.2 (C166S G334D) subunit of human KATP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: SUR1 subunit of human KATP

SupramoleculeName: SUR1 subunit of human KATP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: ATP-sensitive inward rectifier potassium channel 11

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 11 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.622746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLSRKGIIPE EYVLTRLAED PAKPRYRARQ RRARFVSKKG NCNVAHKNIR EQGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMA WWLIAFAHGD LAPSEGTAEP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGSIF ...String:
MLSRKGIIPE EYVLTRLAED PAKPRYRARQ RRARFVSKKG NCNVAHKNIR EQGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMA WWLIAFAHGD LAPSEGTAEP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGSIF MKTAQAHRRA ETLIFSKHAV IALRHGRLCF MLRVGDLRKS MIISATIHMQ VVRKTTSPEG EVVPLHQVDI PM ENGVGGN SIFLVAPLII YHVIDANSPL YDLAPSDLHH HQDLEIIVIL EGVVETTGIT TQARTSYLAD EILWGQRFVP IVA EEDGRY SVDYSKFDNT VKVPTPLCTA RQLDEDHSLL EALTLASARG PLRKRSVPMA KAKPKFSISP DSLS

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Macromolecule #2: ATP-binding cassette sub-family C member 8

MacromoleculeName: ATP-binding cassette sub-family C member 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 177.237266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGPLAFCGSE NHSAAYRVDQ GVLNNGCFVD ALNVVPHVFL LFITFPILFI GWGSQSSKVH IHHSTWLHFP GHNLRWILTF MLLFVLVCE IAEGILSDGV TESHHLHLYM PAGMAFMAAV TSVVYYHNIE TSNFPKLLIA LLVYWTLAFI TKTIKFVKFL D HAIGFSQL ...String:
MGPLAFCGSE NHSAAYRVDQ GVLNNGCFVD ALNVVPHVFL LFITFPILFI GWGSQSSKVH IHHSTWLHFP GHNLRWILTF MLLFVLVCE IAEGILSDGV TESHHLHLYM PAGMAFMAAV TSVVYYHNIE TSNFPKLLIA LLVYWTLAFI TKTIKFVKFL D HAIGFSQL RFCLTGLLVI LYGMLLLVEV NVIRVRRYIF FKTPREVKPP EDLQDLGVRF LQPFVNLLSK GTYWWMNAFI KT AHKKPID LRAIGKLPIA MRALTNYQRL CEAFDAQVRK DIQGTQGARA IWQALSHAFG RRLVLSSTFR ILADLLGFAG PLC IFGIVD HLGKENDVFQ PKTQFLGVYF VSSQEFLANA YVLAVLLFLA LLLQRTFLQA SYYVAIETGI NLRGAIQTKI YNKI MHLST SNLSMGEMTA GQICNLVAID TNQLMWFFFL CPNLWAMPVQ IIVGVILLYY ILGVSALIGA AVIILLAPVQ YFVAT KLSQ AQRSTLEYSN ERLKQTNEML RGIKLLKLYA WENIFRTRVE TTRRKEMTSL RAFAIYTSIS IFMNTAIPIA AVLITF VGH VSFFKEADFS PSVAFASLSL FHILVTPLFL LSSVVRSTVK ALVSVQKLSE FLSSAEIREE QCAPHEPTPQ GPASKYQ AV PLRVVNRKRP AREDCRGLTG PLQSLVPSAD GDADNCCVQI MGGYFTWTPD GIPTLSNITI RIPRGQLTMI VGQVGCGK S SLLLAALGEM QKVSGAVFWS SLPDSEIGED PSPERETATD LDIRKRGPVA YASQKPWLLN ATVEENIIFE SPFNKQRYK MVIEACSLQP DIDILPHGDQ TQIGERGINL SGGQRQRISV ARALYQHANV VFLDDPFSAL DIHLSDHLMQ AGILELLRDD KRTVVLVTH KLQYLPHADW IIAMKDGTIQ REGTLKDFQR SECQLFEHWK TLMNRQDQEL EKETVTERKA TEPPQGLSRA M SSRDGLLQ DEEEEEEEAA ESEEDDNLSS MLHQRAEIPW RACAKYLSSA GILLLSLLVF SQLLKHMVLV AIDYWLAKWT DS ALTLTPA ARNCSLSQEC TLDQTVYAMV FTVLCSLGIV LCLVTSVTVE WTGLKVAKRL HRSLLNRIIL APMRFFETTP LGS ILNRFS SDCNTIDQHI PSTLECLSRS TLLCVSALAV ISYVTPVFLV ALLPLAIVCY FIQKYFRVAS RDLQQLDDTT QLPL LSHFA ETVEGLTTIR AFRYEARFQQ KLLEYTDSNN IASLFLTAAN RWLEVRMEYI GACVVLIAAV TSISNSLHRE LSAGL VGLG LTYALMVSNY LNWMVRNLAD MELQLGAVKR IHGLLKTEAE SYEGLLAPSL IPKNWPDQGK IQIQNLSVRY DSSLKP VLK HVNALIAPGQ KIGICGRTGS GKSSFSLAFF RMVDTFEGHI IIDGIDIAKL PLHTLRSRLS IILQDPVLFS GTIRFNL DP ERKCSDSTLW EALEIAQLKL VVKALPGGLD AIITEGGENF SQGQRQLFCL ARAFVRKTSI FIMDEATASI DMATENIL Q KVVMTAFADR TVVTIAHRVH TILSADLVIV LKRGAILEFD KPEKLLSRKD SVFASFVRAD K

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration6.83 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28719
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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