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- EMDB-64827: Cryo-EM structure of KICSTOR CCC complex (state 4) -

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Basic information

Entry
Database: EMDB / ID: EMD-64827
TitleCryo-EM structure of KICSTOR CCC complex (state 4)
Map datafull map
Sample
  • Complex: KICSTOR CCC complex
    • Protein or peptide: KICSTOR complex protein SZT2
    • Protein or peptide: KICSTOR complex protein ITFG2
    • Protein or peptide: KICSTOR complex protein kaptin
Keywordslipid binding protein / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of superoxide dismutase activity / KICSTOR complex / corpus callosum morphogenesis / germinal center B cell differentiation / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / postsynaptic actin cytoskeleton / stereocilium / pigmentation ...regulation of superoxide dismutase activity / KICSTOR complex / corpus callosum morphogenesis / germinal center B cell differentiation / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / postsynaptic actin cytoskeleton / stereocilium / pigmentation / cellular response to glucose starvation / negative regulation of TORC1 signaling / cellular response to amino acid starvation / actin filament organization / central nervous system development / post-embryonic development / actin filament binding / peroxisome / lamellipodium / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
Kaptin / Integrin-alpha FG-GAP repeat-containing protein 2 / Integrin-alpha FG-GAP repeat-containing protein 2 / Protein SZT2 / Integrin alpha, N-terminal / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
KICSTOR complex protein SZT2 / KICSTOR complex protein ITFG2 / KICSTOR complex protein kaptin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsSu M-Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other government20231120103446003 China
CitationJournal: To Be Published
Title: Cryo-EM structure of KICSTOR CCC complex
Authors: Su M-Y
History
DepositionMay 28, 2025-
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_64827.png

Downloads & links

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Map

FileDownload / File: emd_64827.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 560 pix.
= 476. Å		0.85 Å/pix.
x 560 pix.
= 476. Å		0.85 Å/pix.
x 560 pix.
= 476. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6370225 - 1.7979138
Average (Standard dev.)-0.00075602625 (±0.02097093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 476.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64827_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_64827_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_64827_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KICSTOR CCC complex

EntireName: KICSTOR CCC complex
Components
  • Complex: KICSTOR CCC complex
    • Protein or peptide: KICSTOR complex protein SZT2
    • Protein or peptide: KICSTOR complex protein ITFG2
    • Protein or peptide: KICSTOR complex protein kaptin

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Supramolecule #1: KICSTOR CCC complex

SupramoleculeName: KICSTOR CCC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: KICSTOR complex protein SZT2

MacromoleculeName: KICSTOR complex protein SZT2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 378.453438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASERPEPEV EEAGQVFLLM KKDYRISRNV RLAWFLSHLH QTVQATPQEM LLQSEQELEV LSVLPPGWQP DEPVVPRPFL LVPSTRVTF LAWQYRFVIE LDLSPSTGIV DDSTGEILFD EVFHALSRCL GGLLRPFRVP GSCIDFQPEI YVTIQAYSSI I GLQSHQVL ...String:
MASERPEPEV EEAGQVFLLM KKDYRISRNV RLAWFLSHLH QTVQATPQEM LLQSEQELEV LSVLPPGWQP DEPVVPRPFL LVPSTRVTF LAWQYRFVIE LDLSPSTGIV DDSTGEILFD EVFHALSRCL GGLLRPFRVP GSCIDFQPEI YVTIQAYSSI I GLQSHQVL VQGCLLDPSQ REVFLQQIYE QLCLFEDKVA TMLQQQYDPQ SQAEDQSPDS GDLLGRKVGV SMVTADLGLV SM IRQGILA LQLLPSNSSA GIIVITDGVT SVPDVAVCET LLNQLRSGTV ACSFVQVGGV YSYDCSFGHV PNVELMKFIA MAT FGSYLS TCPEPEPGNL GLTVYHRAFL LYSFLRSGEA LNPEYYCGSQ HRLFNEHLVS ASSNPALALR RKKHTEKEVP ADLV STVSV RLREGYSVRE VTLAKGGSQL EVKLVLLWKH NMRIEYVAMA PWPLEPEGPR VTRVEVTMEG GYDILHDVSC ALRQP IRSL YRTHVIRRFW NTLQSINQTD QMLAHLQSFS SVPEHFTLPD STKSGVPLFY IPPGSTTPVL SLQPSGSDSS HAQFAA YWK PVLSMDANSW QRWLHMHRLV LILEHDTPIP KHLHTPGSNG RYSTIQCRIS HSSLTSLLRD WSSFVLVEGY SYVKLLS SA PDQPPNSFYM VRIISKAPCM VLRLGFPIGT PAPARHKIVS GLREEILRLR FPHRVQSKEP TPKVKRKGLG GAGGGSSP S KSPPVLGPQQ ALSDRPCLVV LHKPLDKLLI RYEKLPLDYR APFLLTLEPP GPLPLVSGRS ASSSLASLSR YLYHQRWLW SVPSGLAPAL PLSAIAQLLS ILTEVRLSEG FHFACSGEGI INMVLELPIQ NEPPGQAAAE EKHTCVVQYI LFPPHSTSTK DSFSTDDDN DVEVEALEGD SELNLVTEVW VEPQYGRVGP GPGIWKHLQD LTYSEIPQAL HPRDAACIGS MLSFEYLIQL C QSKEWGPL PPEPRVSDGL DQGGDTCVHE IPFHFDLMGL LPQCQQLQMF FLLLAREPEG VPFAEGSCPA NDMVLCLLHS CL GQELSDR EIPLTPVDQA AFLSEVLRRT CHVPGAEGPL LGVHGIPKEQ AVGSTQATGD SAFTSLSVGL PETLKPLISA QPP QWRCYA RLVNPQHVFL TFLPATFSDV QRLAACGLEG PPQEETKPKF GDWSGAPSLK DLGGTGIKAT KSHVPVLSVT LASD NAQNQ GELSPPFRRD LQAYAGRQAS QTESADGPRT RCPVYIYSCS LEALREQMVG MQPPQAPRDL IFRTQFLDHP SPSSA WMEP RYKEAANHCA LLQEHAQRCY VRGLFRSLQQ AQSVTSQDLL TAVDACEELL QEIDITPFLL ALCGHTWGLP HAPPSP GPL SPGPFSSSME EGAEPRERAI LASESSIETE DLSEPEFQST RVPGIPDPGP EISLTDVCQL RGEAHGALHS VIQEKFL EI SRLHFRTVPS NPHYFFYCPP SSRREDEGPR DTVDRKISDL EFSEAELMGE EGDTSACCVV TESDPELEVE YRESRESD L GPAGLDSASL SDVDTVNPDE DSFSILGGDS PTGPESFLHD LPPLFLHLTC SVRLRGQHSS VPVCSLPTCL GQVLSSLEG PPVGGRVPLR DLSVTLDVFM LTLPLEVELP TASDPQHHRS TSESSASFPR SPGQPSSLRS DDGLGPPLPP PEEERHPGLS NLATPHRLA IETTMNEIRW LLEDEMVGAL RRGGIPQSPA LHRAAAHIHS SPGRSTCLRQ TLPLSFVFGP ERSLTQFKEE F RRLHLPGH VLLEDPDSGF FFVAAGQQPG GSHGEPSSAA WAWHSHEDRA EGIEGETLTA SPQAPGSPED SEGVPLISLP RV PQGGSQP GPSRGLSLMS SQGSVDSDHL GYDGGSSGSD SEGPNDTLGE KAPFTLRTPP GPAPPQPSLS GLPGPCLPDF WLI VRVLQD RVEVYAHARS LIREDGGPGT ECRHLQQLLV RRVGEICREV NQRLLLQDLH DSHVCNSLLV AESEEDLWRS ETPF HSRQR APLPSDDYAA DESCAPRGYL AATMQFVPGH FSCDVVWGTV IRVHSRLKMG PSMGVSRAIQ ALRSVLNAFS VVNRK NMFV YQERATKAVY YLRLLETSCS DRPWKGDALP PSLALSRSQE PIYSEEASGP RSPLDMVSSR SSDAARPVGQ VDRHIQ LLV HGVGQAGPEI TDELVRVLCR RLDEATLDVI TVMLVRNCKL TPADVEFIQP PGSLPSEVLH LALPTSCRPW LPALAWY LR QNLLIFLHSP KYTDSNSRNH FQHPLPPQGG LPDLDIYLYN KPGGQGTGGK GVACITLAFV DEGGAPLSLA LWPPSSPG P PDPLREEEFE QLTQVIRCPV VVDSSSAQNG APRLRLDVWE KGNISIVQLE EKLRGAARQA LADAIIELQL LPASLCTED TPTGSLRNGS LETKSSAGRA STFPPAPVPG EPVTPPSKAG RRSFWDMLSK TECGDLGSPK TTDDIVLDRP EDTRGRRRHK TESVRTPGG AERAPGSDSG AQRQKRRTTQ LEEGEVGTLH PVFARVAQRW MEFMVQIGCA SVSRSSAHMV SRFLLPSILS E FTALVTSM AGDTSVRIFE QHLGSEPEIF GPCSPGQLGP SPRPAAERHL LLLGRNFLQW RRPTQQAAKA MQRFEPGGDG SS GRNAPRQ RLLLLEVVDK KLQLLTYNWA PDLGAALGRA LVRLVQWQNA RAHLIFCLLS QKLGLFHHYG QLDFPVRDEK EPN PFLLPT MEVETLIRSA SPPLSREQGR LSGSSRGGGP LPLDTFPFDE ALRDITAARP SSVLGPVPRP PDPVTYHGQQ FLEI KMAER RELERQMKME NLFVTWQQRS TPATMPISAG ELETLKQSSR LVHYCATAML FDPAAWLHGP PETSGPPDGQ RRHRP ESGS GSREAPTSCE SLDVSPPGAR EEPWLKELSL AFLQQYVQYL QSIGFVLVPL RPPSPARSTS RPRAMAILGT EGRGSF SCP KTKTDGSPKS TSSPVTTYHL QRALPGGIIL MELAFQGCYF CVKQFALECS RIPMGQAVNS QLSMLFTEEC DKVRDLM HV HSFSYDFHLR LVHQHVLGAH LVLRHGYHLT TFLRHFLAHH PDGPHFGRNH IYQGTLELPT PLIAAHQLYN YVADHASS Y HMKPLRMARP GGPEHNEYAL VSAWHSSGSY LDSEGLRHQD DFDVSLLVCH CAAPFEEQGE AERHVLRLQF FVVLTSQRE LFPRLTADMR RFRKPPRLPP EPEAPGSSAG SPGEASGLIL APGPAPLFPP LAAEVGMARA RLAQLVRLAG GHCRRDTLWK RLFLLEPPG PDRLRLGGRL ALAELEELLE AVHAKSIGDI DPQLDCFLSM TVSWYQSLIK VLLSRFPQSC RHFQSPDLGT Q YLVVLNQK FTDCFVLVFL DSHLGKTSLT VVFREPFPVQ PQDSESPPAQ LVSTYHHLES VINTACFTLW TRLL

UniProtKB: KICSTOR complex protein SZT2

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Macromolecule #2: KICSTOR complex protein ITFG2

MacromoleculeName: KICSTOR complex protein ITFG2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.365742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRSVSYVQRV ALEFSGSLFP HAICLGDVDN DTLNELVVGD TSGKVSVYKN DDSRPWLTCS CQGMLTCVGV GDVCNKGKNL LVAVSAEGW FHLFDLTPAK VLDASGHHET LIGEEQRPVF KQHIPANTKV MLISDIDGDG CRELVVGYTD RVVRAFRWEE L GEGPEHLT ...String:
MRSVSYVQRV ALEFSGSLFP HAICLGDVDN DTLNELVVGD TSGKVSVYKN DDSRPWLTCS CQGMLTCVGV GDVCNKGKNL LVAVSAEGW FHLFDLTPAK VLDASGHHET LIGEEQRPVF KQHIPANTKV MLISDIDGDG CRELVVGYTD RVVRAFRWEE L GEGPEHLT GQLVSLKKWM LEGQVDSLSV TLGPLGLPEL MVSQPGCAYA ILLCTWKKDT GSPPASEGPT DGSRETPAAR DV VLHQTSG RIHNKNVSTH LIGNIKQGHG TESSGSGLFA LCTLDGTLKL MEEMEEADKL LWSVQVDHQL FALEKLDVTG NGH EEVVAC AWDGQTYIID HNRTVVRFQV DENIRAFCAG LYACKEGRNS PCLVYVTFNQ KIYVYWEVQL ERMESTNLVK LLET KPEYH SLLQELGVDP DDLPVTRALL HQTLYHPDQP PQCAPSSLQD PT

UniProtKB: KICSTOR complex protein ITFG2

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Macromolecule #3: KICSTOR complex protein kaptin

MacromoleculeName: KICSTOR complex protein kaptin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.128305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMGEAAVAAG PCPLREDSFT RFSSQSNVYG LAGGAGGRGE LLAATLKGKV LGFRYQDLRQ KIRPVAKELQ FNYIPVDAEI VSIDTFNKS PPKRGLVVGI TFIKDSGDKG SPFLNIYCDY EPGSEYNLDS IAQSCLNLEL QFTPFQLCHA EVQVGDQLET V FLLSGNDP ...String:
MMGEAAVAAG PCPLREDSFT RFSSQSNVYG LAGGAGGRGE LLAATLKGKV LGFRYQDLRQ KIRPVAKELQ FNYIPVDAEI VSIDTFNKS PPKRGLVVGI TFIKDSGDKG SPFLNIYCDY EPGSEYNLDS IAQSCLNLEL QFTPFQLCHA EVQVGDQLET V FLLSGNDP AIHLYKENEG LHQFEEQPVE NLFPELTNLT SSVLWLDVHN FPGTSRRLSA LGCQSGYVRV AHVDQRSREV LQ MWSVLQD GPISRVIVFS LSAAKETKDR PLQDEYSVLV ASMLEPAVVY RDLLNRGLED QLLLPGSDQF DSVLCSLVTD VDL DGRPEV LVATYGQELL CYKYRGPESG LPEAQHGFHL LWQRSFSSPL LAMAHVDLTG DGLQELAVVS LKGVHILQHS LIQA SELVL TRLRHQVEQR RRRLQGLEDG AGAGPAENAA S

UniProtKB: KICSTOR complex protein kaptin

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: alphafold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271421
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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