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- EMDB-62322: Structure of KATP channel in complex with centipede toxin SpTx1 -

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Basic information

Entry
Database: EMDB / ID: EMD-62322
TitleStructure of KATP channel in complex with centipede toxin SpTx1
Map datacomposite map
Sample
  • Complex: KATP in complex with SpTx1
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
    • Protein or peptide: ATP-binding cassette sub-family C member 8 isoform X2
    • Protein or peptide: SpTx1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
KeywordsKATP / Kir6.2 / SUR1 / TRANSPORT PROTEIN / Glibenclamide / SpTx1
Function / homology
Function and homology information


Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / response to resveratrol / inward rectifying potassium channel / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade ...Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / response to resveratrol / inward rectifying potassium channel / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of monoatomic ion transmembrane transport / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / : / ankyrin binding / neuromuscular process / response to ATP / potassium ion import across plasma membrane / potassium ion binding / action potential / voltage-gated potassium channel activity / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / cellular response to nutrient levels / Ion homeostasis / potassium ion transmembrane transport / T-tubule / regulation of insulin secretion / response to ischemia / determination of adult lifespan / regulation of membrane potential / Regulation of insulin secretion / negative regulation of insulin secretion / ADP binding / sarcolemma / ABC-family proteins mediated transport / glucose metabolic process / presynapse / transmembrane transporter binding / response to hypoxia / response to xenobiotic stimulus / apoptotic process / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
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-binding cassette sub-family C member 8 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesHomo sapiens (human) / Mesocricetus auratus (golden hamster) / Scolopendra polymorpha (arthropod)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsChen L / Wang M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
CitationJournal: To Be Published
Title: Structure of KATP in complex with SpTx1
Authors: Chen L / Wang M
History
DepositionNov 8, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62322.png

Downloads & links

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Map

FileDownload / File: emd_62322.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 338.944 Å		1.32 Å/pix.
x 256 pix.
= 338.944 Å		1.32 Å/pix.
x 256 pix.
= 338.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.324 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-0.1524386 - 8.587764
Average (Standard dev.)0.075486064 (±0.21172525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 338.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: consensus map

Fileemd_62322_additional_1.map
Annotationconsensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KATP in complex with SpTx1

EntireName: KATP in complex with SpTx1
Components
  • Complex: KATP in complex with SpTx1
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
    • Protein or peptide: ATP-binding cassette sub-family C member 8 isoform X2
    • Protein or peptide: SpTx1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide

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Supramolecule #1: KATP in complex with SpTx1

SupramoleculeName: KATP in complex with SpTx1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: 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: 43.595723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLSRKGIIPE EYVLTRLAED PAEPRYRARQ RRARFVSKKG NCNVAHKNIR EEGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMA WWLIAFAHGD LAPSEGTAEP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGCIF ...String:
MLSRKGIIPE EYVLTRLAED PAEPRYRARQ RRARFVSKKG NCNVAHKNIR EEGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMA WWLIAFAHGD LAPSEGTAEP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGCIF MKTAQAHRRA ETLIFSKHAV IALRHGRLCF MLRVGDLRKS MIISATIHMQ VVRKTTSPEG EVVPLHQVDI PM ENGVGGN SIFLVAPLII YHVIDANSPL YDLAPSDLHH HQDLEIIVIL EGVVETTGIT TQARTSYLAD EILWGQRFVP IVA EEDGRY SVDYSKFGNT IKVPTPLCTA RQLDEDHSLL EALTLASARG PLRKRSVPMA KAKPKFSISP DSLS

UniProtKB: ATP-sensitive inward rectifier potassium channel 11

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Macromolecule #2: ATP-binding cassette sub-family C member 8 isoform X2

MacromoleculeName: ATP-binding cassette sub-family C member 8 isoform X2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 177.295594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPLAFCGTEN HSAAYRVDQG VLNNGCFVDA LNVVPHVFLL FITFPILFIG WGSQSSKVHI HHSTWLHFPG HNLRWILTFI LLFVLVCEI AEGILSDGVT ESRHLHLYMP AGMAFMAAIT SVVYYHNIET SNFPKLLIAL LIYWTLAFIT KTIKFVKFYD H AIGFSQLR ...String:
MPLAFCGTEN HSAAYRVDQG VLNNGCFVDA LNVVPHVFLL FITFPILFIG WGSQSSKVHI HHSTWLHFPG HNLRWILTFI LLFVLVCEI AEGILSDGVT ESRHLHLYMP AGMAFMAAIT SVVYYHNIET SNFPKLLIAL LIYWTLAFIT KTIKFVKFYD H AIGFSQLR FCLTGLLVIL YGMLLLVEVN VIRVRRYIFF KTPRKVKPPE DLQDLGVRFL QPFVNLLSKG TYWWMNAFIK TA HKKPIDL RAIGKLPIAM RALTNYQRLC VAFDAQARKD TQSPQGARAI WRALCHAFGR RLILSSTFRI LADLLGFAGP LCI FGIVDH LGKENHVFQP KTQFLGVYFV SSQEFLGNAY VLAVLLFLAL LLQRTFLQAS YYVAIETGIN LRGAIQTKIY NKIM HLSTS NLSMGEMTAG QICNLVAIDT NQLMWFFFLC PNLWAMPVQI IVGVILLYYI LGVSALIGAA VIILLAPVQY FVATK LSQA QRSTLEHSNE RLKQTNEMLR GMKLLKLYAW ESIFCSRVEV TRRKEMTSLR AFAVYTSISI FMNTAIPIAA VLITFV GHV SFFKESDLSP SVAFASLSLF HILVTPLFLL SSVVRSTVKA LVSVQKLSEF LSSAEIREEQ CAPREPAPQG QAGKYQA VP LKVVNRKRPA REEVRDLLGP LQRLAPSMDG DADNFCVQII GGFFTWTPDG IPTLSNITIR IPRGQLTMIV GQVGCGKS S LLLATLGEMQ KVSGAVFWNS NLPDSEGEDP SSPERETAAG SDIRSRGPVA YASQKPWLLN ATVEENITFE SPFNKQRYK MVIEACSLQP DIDILPHGDQ TQIGERGINL SGGQRQRISV ARALYQQTNV VFLDDPFSAL DVHLSDHLMQ AGILELLRDD KRTVVLVTH KLQYLPHADW IIAMKDGTIQ REGTLKDFQR SECQLFEHWK TLMNRQDQEL EKETVMERKA SEPSQGLPRA M SSRDGLLL DEEEEEEEAA ESEEDDNLSS VLHQRAKIPW RACTKYLSSA GILLLSLLVF SQLLKHMVLV AIDYWLAKWT DS ALVLSPA ARNCSLSQEC DLDQSVYAMV FTLLCSLGIV LCLVTSVTVE WTGLKVAKRL HRSLLNRIIL APMRFFETTP LGS ILNRFS SDCNTIDQHI PSTLECLSRS TLLCVSALTV ISYVTPVFLV ALLPLAVVCY FIQKYFRVAS RDLQQLDDTT QLPL LSHFA ETVEGLTTIR AFRYEARFQQ KLLEYTDSNN IASLFLTAAN RWLEVRMEYI GACVVLIAAA TSISNSLHRE LSAGL VGLG LTYALMVSNY LNWMVRNLAD MEIQLGAVKR IHALLKTEAE SYEGLLAPSL IPKNWPDQGK IQIQNLSVRY DSSLKP VLK HVNALISPGQ KIGICGRTGS GKSSFSLAFF RMVDMFEGRI IIDGIDIAKL PLHTLRSRLS IILQDPVLFS GTIRFNL DP EKKCSDSTLW EALEIAQLKL VVKALPGGLD AIITEGGENF SQGQRQLFCL ARAFVRKTSI FIMDEATASI DMATENIL Q KVVMTAFADR TVVTIAHRVH TILSADLVMV LKRGAILEFD KPETLLSQKD SVFASFVRAD K

UniProtKB: ATP-binding cassette sub-family C member 8

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Macromolecule #3: SpTx1

MacromoleculeName: SpTx1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Scolopendra polymorpha (arthropod)
Molecular weightTheoretical: 6.527552 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSADLIKKKL PFRTRSKFPR KSECVQDCAK AFTNGNKDKI KDVKSEFFSC YCWYEA

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #5: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-...

MacromoleculeName: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
type: ligand / ID: 5 / Number of copies: 4 / Formula: GBM
Molecular weightTheoretical: 494.004 Da
Chemical component information

ChemComp-GBM:
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246583
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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