[English] 日本語
Yorodumi
- EMDB-72381: The dimeric KICSTOR-GATOR1 supercomplex (constitutive GATOR1 dime... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72381
TitleThe dimeric KICSTOR-GATOR1 supercomplex (constitutive GATOR1 dimer, SZT2 fragment)
Map dataComposite map of constitutive GATOR1 dimer bound to SZT2 N-terminal 1-1330 fragment.
Sample
  • Complex: Dimeric supercomplex of KICSTOR-GATOR1 (constitutive GATOR1 dimer, N-terminal SZT2 fragment)
    • Complex: dimeric constitutive GATOR1 subcomplex
      • Protein or peptide: Tandem DEPDC5-DEPDC5
      • Protein or peptide: NPRL2
      • Protein or peptide: NPRL3
      • Protein or peptide: NPRL2
      • Protein or peptide: NPRL3
    • Complex: N-terminal fragment (1-1330) of the SZT2 component of the KICSTOR subcomplex
      • Protein or peptide: SZT2 1-1330 N-terminal fragment
      • Protein or peptide: SZT2 1-1330 N-terminal fragment
KeywordsLysosome / GATOR1 / KICSTOR / cell growth / amino acid sensing / mTOR / KPTN / ITFG2 / C12orf66 / SZT2 / NPRL2 / NPRL3 / DEPDC5 / CELL CYCLE
Function / homology
Function and homology information


KICSTOR complex / regulation of superoxide dismutase activity / GATOR1 complex / negative regulation of kinase activity / corpus callosum morphogenesis / aorta morphogenesis / protein localization to lysosome / Amino acids regulate mTORC1 / cardiac muscle tissue development / vacuolar membrane ...KICSTOR complex / regulation of superoxide dismutase activity / GATOR1 complex / negative regulation of kinase activity / corpus callosum morphogenesis / aorta morphogenesis / protein localization to lysosome / Amino acids regulate mTORC1 / cardiac muscle tissue development / vacuolar membrane / ventricular septum development / pigmentation / roof of mouth development / cellular response to glucose starvation / negative regulation of TORC1 signaling / positive regulation of autophagy / cellular response to amino acid starvation / GTPase activator activity / post-embryonic development / central nervous system development / peroxisome / lysosomal membrane
Similarity search - Function
Protein SZT2 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / : / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / GATOR1 complex protein NPRL3, C-terminal HTH
Similarity search - Domain/homology
GATOR1 complex protein NPRL3 / KICSTOR complex protein SZT2 / GATOR1 complex protein NPRL2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBayly-Jones C / Lupton CJ / Chang YG / Ellisdon AM
Funding support Australia, 4 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2036864 Australia
Australian Research Council (ARC)DE240100992 Australia
Other governmentMCRF21036
Australian Research Council (ARC)LE170100016 Australia
CitationJournal: To Be Published
Title: Structure of the lysosomal KICSTOR-GATOR1 nutrient-sensing supercomplex
Authors: Bayly-Jones C / Lupton CJ / Chang YG / Ellisdon AM
History
DepositionAug 28, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72381.png

Downloads & links

-
Map

FileReleased
AnnotationComposite map of constitutive GATOR1 dimer bound to SZT2 N-terminal 1-1330 fragment.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å		1 Å/pix.
x 320 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum0.0 - 11.385176
Average (Standard dev.)0.072934136 (±0.53286326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Dimeric supercomplex of KICSTOR-GATOR1 (constitutive GATOR1 dimer...

EntireName: Dimeric supercomplex of KICSTOR-GATOR1 (constitutive GATOR1 dimer, N-terminal SZT2 fragment)
Components
  • Complex: Dimeric supercomplex of KICSTOR-GATOR1 (constitutive GATOR1 dimer, N-terminal SZT2 fragment)
    • Complex: dimeric constitutive GATOR1 subcomplex
      • Protein or peptide: Tandem DEPDC5-DEPDC5
      • Protein or peptide: NPRL2
      • Protein or peptide: NPRL3
      • Protein or peptide: NPRL2
      • Protein or peptide: NPRL3
    • Complex: N-terminal fragment (1-1330) of the SZT2 component of the KICSTOR subcomplex
      • Protein or peptide: SZT2 1-1330 N-terminal fragment
      • Protein or peptide: SZT2 1-1330 N-terminal fragment

+
Supramolecule #1: Dimeric supercomplex of KICSTOR-GATOR1 (constitutive GATOR1 dimer...

SupramoleculeName: Dimeric supercomplex of KICSTOR-GATOR1 (constitutive GATOR1 dimer, N-terminal SZT2 fragment)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 582 KDa

+
Supramolecule #2: dimeric constitutive GATOR1 subcomplex

SupramoleculeName: dimeric constitutive GATOR1 subcomplex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5-#6
Details: Single copy of a tandem DEPDC5-DEPDC5 constitutive dimer, bound to two copies each of NPRL2 and NPRL3
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: N-terminal fragment (1-1330) of the SZT2 component of the KICSTOR...

SupramoleculeName: N-terminal fragment (1-1330) of the SZT2 component of the KICSTOR subcomplex
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4, #7
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Tandem DEPDC5-DEPDC5

MacromoleculeName: Tandem DEPDC5-DEPDC5 / type: protein_or_peptide / ID: 1
Details: Tandem fusion of DEPDC5 connected by long, flexible linker. Forms a constitutive dimer of the GATOR1 complex when NPRL2, NPRL3 are present.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDYKDDDDK GGGGGASTMR TTKVYKLVIH KKGFGGSDDE LVVNPKVFPH IKLGDIVEIA HPNDEYSPLL LQVKSLKEDL QKETISVDQT VTQVFRLRP YQDVYVNVVD PKDVTLDLVE LTFKDQYIGR GDMWRLKKSL VSTCAYITQK VEFAGIRAQA GELWVKNEKV ...String:
MGDYKDDDDK GGGGGASTMR TTKVYKLVIH KKGFGGSDDE LVVNPKVFPH IKLGDIVEIA HPNDEYSPLL LQVKSLKEDL QKETISVDQT VTQVFRLRP YQDVYVNVVD PKDVTLDLVE LTFKDQYIGR GDMWRLKKSL VSTCAYITQK VEFAGIRAQA GELWVKNEKV MCGYISEDTR VVFRSTSAMV YIFIQMSCE MWDFDIYGDL YFEKAVNGFL ADLFTKWKEK NCSHEVTVVL FSRTFYDAKS VDEFPEINRA SIRQDHKGRF YEDFYKVVVQ NERREEWTSL LVTIKKLFI QYPVLVRLEQ AEGFPQGDNS TSAQGNYLEA INLSFNVFDK HYINRNFDRT GQMSVVITPG VGVFEVDRLL MILTKQRMID NGIGVDLVCM GEQPLHAVP LFKLHNRSAP RDSRLGDDYN IPHWINHSFY TSKSQLFCNS FTPRIKLAGK KPASEKAKNG RDTSLGSPKE SENALPIQVD YDAYDAQVFR LPGPSRAQC LTTCRSVRER ESHSRKSASS CDVSSSPSLP SRTLPTEEVR SQASDDSSLG KSANILMIPH PHLHQYEVSS SLGYTSTRDV LENMMEPPQR DSSAPGRFH VGSAESMLHV RPGGYTPQRA LINPFAPSRM PMKLTSNRRR WMHTFPVGPS GEAIQIHHQT RQNMAELQGS GQRDPTHSSA ELLELAYHEA AGRHSNSRQ PGDGMSFLNF SGTEELSVGL LSNSGAGMNP RTQNKDSLED SVSTSPDPIL TLSAPPVVPG FCCTVGVDWK SLTTPACLPL TTDYFPDRQG LQNDYTEGC YDLLPEADID RRDEDGVQMT AQQVFEEFIC QRLMQGYQII VQPKTQKPNP AVPPPLSSSP LYSRGLVSRN RPEEEDQYWL SMGRTFHKVT LKDKMITVT RYLPKYPYES AQIHYTYSLC PSHSDSEFVS CWVEFSHERL EEYKWNYLDQ YICSAGSEDF SLIESLKFWR TRFLLLPACV TATKRITEGE AHCDIYGDR PRADEDEWQL LDGFVRFVEG LNRIRRRHRS DRMMRKGTAM KGLQMTGPIS THSLESTAPP VGKKGTSALS ALLEMEASQK CLGEQQAAVH GGKSSAQSA ESSSVAMTPT YMDSPRKDGA FFMEFVRSPR TASSAFYPQV SVDQTATPML DGTSLGICTG QSMDRGNSQT FGNSQNIGEQ GYSSTNSSDS SSQQLVASS LTSSSTLTEI LEAMKHPSTG VQLLSEQKGL SPYCFISAEV VHWLVNHVEG IQTQAMAIDI MQKMLEEQLI THASGEAWRT FIYGFYFYKI VTDKEPDRV AMQQPATTWH TAGVDDFASF QRKWFEVAFV AEELVHSEIP AFLLPWLPSR PASYASRHSS FSRSFGGRSQ AAALLAATVP EQRTVTLDVD VNNRTDRLE WCSCYYHGNF SLNAAFEIKL HWMAVTAAVL FEMVQGWHRK ATSCGFLLVP VLEGPFALPS YLYGDPLRAQ LFIPLNISCL LKEGSEHLFD SFEPETYWD RMHLFQEAIA HRFGFVQDKY SASAFNFPAE NKPQYIHVTG TVFLQLPYSK RKFSGQQRRR RNSTSSTNQN MFCEERVGYN WAYNTMLTKT WRSSATGDE KFADRLLKDF TDFCINRDNR LVTFWTSCLE KMHASAPGGA SGSYYRAEKG QGSGAEPQSG HSSRGSGSFV KFFTYSTQPT GSGGGMASMG HTGLKGGSG GDSQCGTSMS GQESGQGGGG GQGGDGGVGL SGIGGGAGAT DSGIPGLGVS GGENGGKASP GGTPAPKMMT TQSTCGFNGG STGLGGTGSG QMGKGRSTM RTTKVYKLVI HKKGFGGSDD ELVVNPKVFP HIKLGDIVEI AHPNDEYSPL LLQVKSLKED LQKETISVDQ TVTQVFRLRP YQDVYVNVVD PKDVTLDLV ELTFKDQYIG RGDMWRLKKS LVSTCAYITQ KVEFAGIRAQ AGELWVKNEK VMCGYISEDT RVVFRSTSAM VYIFIQMSCE MWDFDIYGDL YFEKAVNGF LADLFTKWKE KNCSHEVTVV LFSRTFYDAK SVDEFPEINR ASIRQDHKGR FYEDFYKVVV QNERREEWTS LLVTIKKLFI QYPVLVRLEQ AEGFPQGDN STSAQGNYLE AINLSFNVFD KHYINRNFDR TGQMSVVITP GVGVFEVDRL LMILTKQRMI DNGIGVDLVC MGEQPLHAVP LFKLHNRSAP RDSRLGDDY NIPHWINHSF YTSKSQLFCN SFTPRIKLAG KKPASEKAKN GRDTSLGSPK ESENALPIQV DYDAYDAQVF RLPGPSRAQC LTTCRSVRER ESHSRKSAS SCDVSSSPSL PSRTLPTEEV RSQASDDSSL GKSANILMIP HPHLHQYEVS SSLGYTSTRD VLENMMEPPQ RDSSAPGRFH VGSAESMLHV RPGGYTPQR ALINPFAPSR MPMKLTSNRR RWMHTFPVGP SGEAIQIHHQ TRQNMAELQG SGQRDPTHSS AELLELAYHE AAGRHSNSRQ PGDGMSFLNF SGTEELSVG LLSNSGAGMN PRTQNKDSLE DSVSTSPDPI LTLSAPPVVP GFCCTVGVDW KSLTTPACLP LTTDYFPDRQ GLQNDYTEGC YDLLPEADID RRDEDGVQM TAQQVFEEFI CQRLMQGYQI IVQPKTQKPN PAVPPPLSSS PLYSRGLVSR NRPEEEDQYW LSMGRTFHKV TLKDKMITVT RYLPKYPYES AQIHYTYSL CPSHSDSEFV SCWVEFSHER LEEYKWNYLD QYICSAGSED FSLIESLKFW RTRFLLLPAC VTATKRITEG EAHCDIYGDR PRADEDEWQL LDGFVRFVE GLNRIRRRHR SDRMMRKGTA MKGLQMTGPI STHSLESTAP PVGKKGTSAL SALLEMEASQ KCLGEQQAAV HGGKSSAQSA ESSSVAMTPT YMDSPRKDG AFFMEFVRSP RTASSAFYPQ VSVDQTATPM LDGTSLGICT GQSMDRGNSQ TFGNSQNIGE QGYSSTNSSD SSSQQLVASS LTSSSTLTEI LEAMKHPST GVQLLSEQKG LSPYCFISAE VVHWLVNHVE GIQTQAMAID IMQKMLEEQL ITHASGEAWR TFIYGFYFYK IVTDKEPDRV AMQQPATTWH TAGVDDFAS FQRKWFEVAF VAEELVHSEI PAFLLPWLPS RPASYASRHS SFSRSFGGRS QAAALLAATV PEQRTVTLDV DVNNRTDRLE WCSCYYHGNF SLNAAFEIK LHWMAVTAAV LFEMVQGWHR KATSCGFLLV PVLEGPFALP SYLYGDPLRA QLFIPLNISC LLKEGSEHLF DSFEPETYWD RMHLFQEAIA HRFGFVQDK YSASAFNFPA ENKPQYIHVT GTVFLQLPYS KRKFSGQQRR RRNSTSSTNQ NMFCEERVGY NWAYNTMLTK TWRSSATGDE KFADRLLKDF TDFCINRDN RLVTFWTSCL EKMHASAP

+
Macromolecule #2: NPRL2

MacromoleculeName: NPRL2 / type: protein_or_peptide / ID: 2 / Details: Wild-type NPRL2 construct / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGYPYDVPDY ADLNGGGGGS TMGSGCRIEC IFFSEFHPTL GPKITYQVPE DFISRELFDT VQVYIITKPE LQNKLITVTA MEKKLIGCPV CIEHKKYSR NALLFNLGFV CDAQAKTCAL EPIVKKLAGY LTTLELESSF VSMEESKQKL VPIMTILLEE LNASGRCTLP ...String:
MGYPYDVPDY ADLNGGGGGS TMGSGCRIEC IFFSEFHPTL GPKITYQVPE DFISRELFDT VQVYIITKPE LQNKLITVTA MEKKLIGCPV CIEHKKYSR NALLFNLGFV CDAQAKTCAL EPIVKKLAGY LTTLELESSF VSMEESKQKL VPIMTILLEE LNASGRCTLP IDESNTIHLK VIEQRPDPPV AQEYDVPVF TKDKEDFFNS QWDLTTQQIL PYIDGFRHIQ KISAEADVEL NLVRIAIQNL LYYGVVTLVS ILQYSNVYCP TPKVQDLVDD KSLQEACLSY VTKQGHKRA SLRDVFQLYC SLSPGTTVRD LIGRHPQQLQ HVDERKLIQF GLMKNLIRRL QKYPVRVTRE EQSHPARLYT GCHSYDEICC KTGMSYHELD ERLENDPNI IICWK

UniProtKB: GATOR1 complex protein NPRL2

+
Macromolecule #3: NPRL3

MacromoleculeName: NPRL3 / type: protein_or_peptide / ID: 3 / Details: Wild-type NPRL3 construct / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGYPYDVPDY ADLNGGGGGS TMRDNTSPIS VILVSSGSRG NKLLFRYPFQ RSQEHPASQT SKPRSRYAAS NTGDHADEQD GDSRFSDVIL ATILATKSE MCGQKFELKI DNVRFVGHPT LLQHALGQIS KTDPSPKREA PTMILFNVVF ALRANADPSV INCLHNLSRR ...String:
MGYPYDVPDY ADLNGGGGGS TMRDNTSPIS VILVSSGSRG NKLLFRYPFQ RSQEHPASQT SKPRSRYAAS NTGDHADEQD GDSRFSDVIL ATILATKSE MCGQKFELKI DNVRFVGHPT LLQHALGQIS KTDPSPKREA PTMILFNVVF ALRANADPSV INCLHNLSRR IATVLQHEER RCQYLTREAK LILALQDEV SAMADGNEGP QSPFHHILPK CKLARDLKEA YDSLCTSGVV RLHINSWLEV SFCLPHKIHY AASSLIPPEA IERSLKAIRP YHALLLLSDE KSLLGELPI DCSPALVRVI KTTSAVKNLQ QLAQDADLAL LQVFQLAAHL VYWGKAIIIY PLCENNVYML SPNASVCLYS PLAEQFSHQF PSHDLPSVLA KFSLPVSLS EFRNPLAPAV QETQLIQMVV WMLQRRLLIQ LHTYVCLMAS PSEEEPRPRE DDVPFTARVG GRSLSTPNAL SFGSPTSSDD MTLTSPSMDN SSAELLPSG DSPLNQRMTE NLLASLSEHE RAAILSVPAA QNPEDLRMFA RLLHYFRGRH HLEEIMYNEN TRRSQLLMLF DKFRSVLVVT THEDPVIAVF QALLP

UniProtKB: GATOR1 complex protein NPRL3

+
Macromolecule #4: SZT2 1-1330 N-terminal fragment

MacromoleculeName: SZT2 1-1330 N-terminal fragment / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDYKDDDDK GGGGGASTMA SERPEPEVEE AGQVFLLMKK DYRISRNVRL AWFLSHLHQT VQATPQEMLL QSEQELEVLS VLPPGWQPDE PVVPRPFLLV PSTRVTFLAW QYRFVIELDL SPSTGIVDDS TGEILFDEVF HALSRCLGGL LRPFRVPGSC IDFQPEIYVT ...String:
MGDYKDDDDK GGGGGASTMA SERPEPEVEE AGQVFLLMKK DYRISRNVRL AWFLSHLHQT VQATPQEMLL QSEQELEVLS VLPPGWQPDE PVVPRPFLLV PSTRVTFLAW QYRFVIELDL SPSTGIVDDS TGEILFDEVF HALSRCLGGL LRPFRVPGSC IDFQPEIYVT IQAYSSIIGL QSHQVLVQGC LLDPSQREVF LQQIYEQLCL FEDKVATMLQ QQYDPQSQAE DQSPDSGDLL GRKVGVSMVT ADLGLVSMIR QGILALQLLP SNSSAGIIVI TDGVTSVPDV AVCETLLNQL RSGTVACSFV QVGGVYSYDC SFGHVPNVEL MKFIAMATFG SYLSTCPEPE PGNLGLTVYH RAFLLYSFLR SGEALNPEYY CGSQHRLFNE HLVSASSNPA LALRRKKHTE KEVPADLVST VSVRLREGYS VREVTLAKGG SQLEVKLVLL WKHNMRIEYV AMAPWPLEPE GPRVTRVEVT MEGGYDILHD VSCALRQPIR SLYRTHVIRR FWNTLQSINQ TDQMLAHLQS FSSVPEHFTL PDSTKSGVPL FYIPPGSTTP VLSLQPSGSD SSHAQFAAYW KPVLSMDANS WQRWLHMHRL VLILEHDTPI PKHLHTPGSN GRYSTIQCRI SHSSLTSLLR DWSSFVLVEG YSYVKLLSSA PDQPPNSFYM VRIISKAPCM VLRLGFPIGT PAPARHKIVS GLREEILRLR FPHRVQSKEP TPKVKRKGLG GAGGGSSPSK SPPVLGPQQA LSDRPCLVVL HKPLDKLLIR YEKLPLDYRA PFLLTLEPPG PLPLVSGRSA SSSLASLSRY LYHQRWLWSV PSGLAPALPL SAIAQLLSIL TEVRLSEGFH FACSGEGIIN MVLELPIQNE PPGQAAAEEK HTCVVQYILF PPHSTSTKDS FSTDDDNDVE VEALEGDSEL NLVTEVWVEP QYGRVGPGPG IWKHLQDLTY SEIPQALHPR DAACIGSMLS FEYLIQLCQS KEWGPLPPEP RVSDGLDQGG DTCVHEIPFH FDLMGLLPQC QQLQMFFLLL AREPEGVPFA EGSCPANDMV LCLLHSCLGQ ELSDREIPLT PVDQAAFLSE VLRRTCHVPG AEGPLLGVHG IPKEQAVGST QATGDSAFTS LSVGLPETLK PLISAQPPQW RCYARLVNPQ HVFLTFLPAT FSDVQRLAAC GLEGPPQEET KPKFGDWSGA PSLKDLGGTG IKATKSHVPV LSVTLASDNA QNQGELSPPF RRDLQAYAGR QASQTESADG PRTRCPVYIY SCSLEALREQ MVGMQPPQAP RDLIFRTQFL DHPSPSSAWM EPRYKEAANH CALLQEHAQR CYVRGLFRSL QQAQSVTSQD LLTAVDAC

UniProtKB: KICSTOR complex protein SZT2

+
Macromolecule #5: NPRL2

MacromoleculeName: NPRL2 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGYPYDVPDY ADLNGGGGGS TMGSGCRIEC IFFSEFHPTL GPKITYQVPE DFISRELFDT VQVYIITKPE LQNKLITVTA MEKKLIGCPV CIEHKKYSR NALLFNLGFV CDAQAKTCAL EPIVKKLAGY LTTLELESSF VSMEESKQKL VPIMTILLEE LNASGRCTLP ...String:
MGYPYDVPDY ADLNGGGGGS TMGSGCRIEC IFFSEFHPTL GPKITYQVPE DFISRELFDT VQVYIITKPE LQNKLITVTA MEKKLIGCPV CIEHKKYSR NALLFNLGFV CDAQAKTCAL EPIVKKLAGY LTTLELESSF VSMEESKQKL VPIMTILLEE LNASGRCTLP IDESNTIHLK VIEQRPDPPV AQEYDVPVF TKDKEDFFNS QWDLTTQQIL PYIDGFRHIQ KISAEADVEL NLVRIAIQNL LYYGVVTLVS ILQYSNVYCP TPKVQDLVDD KSLQEACLSY VTKQGHKRA SLRDVFQLYC SLSPGTTVRD LIGRHPQQLQ HVDERKLIQF GLMKNLIRRL QKYPVRVTRE EQSHPARLYT GCHSYDEICC KTGMSYHELD ERLENDPNI IICWK

+
Macromolecule #6: NPRL3

MacromoleculeName: NPRL3 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGYPYDVPDY ADLNGGGGGS TMRDNTSPIS VILVSSGSRG NKLLFRYPFQ RSQEHPASQT SKPRSRYAAS NTGDHADEQD GDSRFSDVIL ATILATKSE MCGQKFELKI DNVRFVGHPT LLQHALGQIS KTDPSPKREA PTMILFNVVF ALRANADPSV INCLHNLSRR ...String:
MGYPYDVPDY ADLNGGGGGS TMRDNTSPIS VILVSSGSRG NKLLFRYPFQ RSQEHPASQT SKPRSRYAAS NTGDHADEQD GDSRFSDVIL ATILATKSE MCGQKFELKI DNVRFVGHPT LLQHALGQIS KTDPSPKREA PTMILFNVVF ALRANADPSV INCLHNLSRR IATVLQHEER RCQYLTREAK LILALQDEV SAMADGNEGP QSPFHHILPK CKLARDLKEA YDSLCTSGVV RLHINSWLEV SFCLPHKIHY AASSLIPPEA IERSLKAIRP YHALLLLSDE KSLLGELPI DCSPALVRVI KTTSAVKNLQ QLAQDADLAL LQVFQLAAHL VYWGKAIIIY PLCENNVYML SPNASVCLYS PLAEQFSHQF PSHDLPSVLA KFSLPVSLS EFRNPLAPAV QETQLIQMVV WMLQRRLLIQ LHTYVCLMAS PSEEEPRPRE DDVPFTARVG GRSLSTPNAL SFGSPTSSDD MTLTSPSMDN SSAELLPSG DSPLNQRMTE NLLASLSEHE RAAILSVPAA QNPEDLRMFA RLLHYFRGRH HLEEIMYNEN TRRSQLLMLF DKFRSVLVVT THEDPVIAVF QALLP

+
Macromolecule #7: SZT2 1-1330 N-terminal fragment

MacromoleculeName: SZT2 1-1330 N-terminal fragment / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDYKDDDDK GGGGGASTMA SERPEPEVEE AGQVFLLMKK DYRISRNVRL AWFLSHLHQT VQATPQEMLL QSEQELEVLS VLPPGWQPDE PVVPRPFLLV PSTRVTFLAW QYRFVIELDL SPSTGIVDDS TGEILFDEVF HALSRCLGGL LRPFRVPGSC IDFQPEIYVT ...String:
MGDYKDDDDK GGGGGASTMA SERPEPEVEE AGQVFLLMKK DYRISRNVRL AWFLSHLHQT VQATPQEMLL QSEQELEVLS VLPPGWQPDE PVVPRPFLLV PSTRVTFLAW QYRFVIELDL SPSTGIVDDS TGEILFDEVF HALSRCLGGL LRPFRVPGSC IDFQPEIYVT IQAYSSIIGL QSHQVLVQGC LLDPSQREVF LQQIYEQLCL FEDKVATMLQ QQYDPQSQAE DQSPDSGDLL GRKVGVSMVT ADLGLVSMIR QGILALQLLP SNSSAGIIVI TDGVTSVPDV AVCETLLNQL RSGTVACSFV QVGGVYSYDC SFGHVPNVEL MKFIAMATFG SYLSTCPEPE PGNLGLTVYH RAFLLYSFLR SGEALNPEYY CGSQHRLFNE HLVSASSNPA LALRRKKHTE KEVPADLVST VSVRLREGYS VREVTLAKGG SQLEVKLVLL WKHNMRIEYV AMAPWPLEPE GPRVTRVEVT MEGGYDILHD VSCALRQPIR SLYRTHVIRR FWNTLQSINQ TDQMLAHLQS FSSVPEHFTL PDSTKSGVPL FYIPPGSTTP VLSLQPSGSD SSHAQFAAYW KPVLSMDANS WQRWLHMHRL VLILEHDTPI PKHLHTPGSN GRYSTIQCRI SHSSLTSLLR DWSSFVLVEG YSYVKLLSSA PDQPPNSFYM VRIISKAPCM VLRLGFPIGT PAPARHKIVS GLREEILRLR FPHRVQSKEP TPKVKRKGLG GAGGGSSPSK SPPVLGPQQA LSDRPCLVVL HKPLDKLLIR YEKLPLDYRA PFLLTLEPPG PLPLVSGRSA SSSLASLSRY LYHQRWLWSV PSGLAPALPL SAIAQLLSIL TEVRLSEGFH FACSGEGIIN MVLELPIQNE PPGQAAAEEK HTCVVQYILF PPHSTSTKDS FSTDDDNDVE VEALEGDSEL NLVTEVWVEP QYGRVGPGPG IWKHLQDLTY SEIPQALHPR DAACIGSMLS FEYLIQLCQS KEWGPLPPEP RVSDGLDQGG DTCVHEIPFH FDLMGLLPQC QQLQMFFLLL AREPEGVPFA EGSCPANDMV LCLLHSCLGQ ELSDREIPLT PVDQAAFLSE VLRRTCHVPG AEGPLLGVHG IPKEQAVGST QATGDSAFTS LSVGLPETLK PLISAQPPQW RCYARLVNPQ HVFLTFLPAT FSDVQRLAAC GLEGPPQEET KPKFGDWSGA PSLKDLGGTG IKATKSHVPV LSVTLASDNA QNQGELSPPF RRDLQAYAGR QASQTESADG PRTRCPVYIY SCSLEALREQ MVGMQPPQAP RDLIFRTQFL DHPSPSSAWM EPRYKEAANH CALLQEHAQR CYVRGLFRSL QQAQSVTSQD LLTAVDAC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 1.2 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: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 875325
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 356922
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10

-
Atomic model buiding 1

Initial modelPDB ID:

9o5e


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: DEPDC5 interface as starting model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more