[English] 日本語
Yorodumi
- EMDB-64665: Cryo-EM structure of GATOR1-KICSTOR complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64665
TitleCryo-EM structure of GATOR1-KICSTOR complex
Map datafull map for GATOR1-KICSTOR complex
Sample
  • Complex: Complex of GATOR1 bound to KICSTOR
    • Protein or peptide: GATOR1 complex protein NPRL2
    • Protein or peptide: GATOR1 complex protein NPRL3
    • Protein or peptide: GATOR1 complex protein DEPDC5
    • Protein or peptide: KICSTOR complex protein SZT2
KeywordsGAP / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of superoxide dismutase activity / KICSTOR complex / 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 ...regulation of superoxide dismutase activity / KICSTOR complex / 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 / GTPase activator activity / cellular response to amino acid starvation / central nervous system development / post-embryonic development / small GTPase binding / peroxisome / lysosome / intracellular signal transduction / lysosomal membrane / protein-containing complex binding / perinuclear region of cytoplasm / cytosol
Similarity search - Function
Protein SZT2 / : / IML1 N-terminal double psi beta barrel domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / : / Nitrogen Permease regulator of amino acid transport activity 3 ...Protein SZT2 / : / IML1 N-terminal double psi beta barrel domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / : / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1, N-terminal domain / DEPDC5 protein C-terminal region / GATOR1 complex protein NPRL3, C-terminal HTH / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GATOR1 complex protein DEPDC5 / 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: 2.97 Å
AuthorsSu M-Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other government20231120103446003 China
CitationJournal: To Be Published
Title: Cryo-EM structure of GATOR1-KICSTOR complex
Authors: Su M-Y
History
DepositionMay 18, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64665.png

Downloads & links

-
Map

FileDownload / File: emd_64665.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map for GATOR1-KICSTOR complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. 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: 0.075
Minimum - Maximum-0.76807207 - 1.6094395
Average (Standard dev.)-0.00026431444 (±0.019983469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 510.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64665_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: local refinement on Nprl3-SZT2 portion

Fileemd_64665_additional_1.map
Annotationlocal refinement on Nprl3-SZT2 portion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: mask for local refine (Nprl3-SZT2)

Fileemd_64665_additional_2.map
Annotationmask for local refine (Nprl3-SZT2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B for GATOR1-KICSTOR complex

Fileemd_64665_half_map_1.map
Annotationhalf map B for GATOR1-KICSTOR complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A for GATOR1-KICSTOR complex

Fileemd_64665_half_map_2.map
Annotationhalf map A for GATOR1-KICSTOR complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of GATOR1 bound to KICSTOR

EntireName: Complex of GATOR1 bound to KICSTOR
Components
  • Complex: Complex of GATOR1 bound to KICSTOR
    • Protein or peptide: GATOR1 complex protein NPRL2
    • Protein or peptide: GATOR1 complex protein NPRL3
    • Protein or peptide: GATOR1 complex protein DEPDC5
    • Protein or peptide: KICSTOR complex protein SZT2

-
Supramolecule #1: Complex of GATOR1 bound to KICSTOR

SupramoleculeName: Complex of GATOR1 bound to KICSTOR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 815 KDa

-
Macromolecule #1: GATOR1 complex protein NPRL2

MacromoleculeName: GATOR1 complex protein NPRL2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.711395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSGCRIECI FFSEFHPTLG PKITYQVPED FISRELFDTV QVYIITKPEL QNKLITVTAM EKKLIGCPVC IEHKKYSRNA LLFNLGFVC DAQAKTCALE PIVKKLAGYL TTLELESSFV SMEESKQKLV PIMTILLEEL NASGRCTLPI DESNTIHLKV I EQRPDPPV ...String:
MGSGCRIECI FFSEFHPTLG PKITYQVPED FISRELFDTV QVYIITKPEL QNKLITVTAM EKKLIGCPVC IEHKKYSRNA LLFNLGFVC DAQAKTCALE PIVKKLAGYL TTLELESSFV SMEESKQKLV PIMTILLEEL NASGRCTLPI DESNTIHLKV I EQRPDPPV AQEYDVPVFT KDKEDFFNSQ WDLTTQQILP YIDGFRHIQK ISAEADVELN LVRIAIQNLL YYGVVTLVSI LQ YSNVYCP TPKVQDLVDD KSLQEACLSY VTKQGHKRAS LRDVFQLYCS LSPGTTVRDL IGRHPQQLQH VDERKLIQFG LMK NLIRRL QKYPVRVTRE EQSHPARLYT GCHSYDEICC KTGMSYHELD ERLENDPNII ICWK

UniProtKB: GATOR1 complex protein NPRL2

-
Macromolecule #2: GATOR1 complex protein NPRL3

MacromoleculeName: GATOR1 complex protein NPRL3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.68082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRDNTSPISV ILVSSGSRGN KLLFRYPFQR SQEHPASQTS KPRSRYAASN TGDHADEQDG DSRFSDVILA TILATKSEMC GQKFELKID NVRFVGHPTL LQHALGQISK TDPSPKREAP TMILFNVVFA LRANADPSVI NCLHNLSRRI ATVLQHEERR C QYLTREAK ...String:
MRDNTSPISV ILVSSGSRGN KLLFRYPFQR SQEHPASQTS KPRSRYAASN TGDHADEQDG DSRFSDVILA TILATKSEMC GQKFELKID NVRFVGHPTL LQHALGQISK TDPSPKREAP TMILFNVVFA LRANADPSVI NCLHNLSRRI ATVLQHEERR C QYLTREAK LILALQDEVS AMADGNEGPQ SPFHHILPKC KLARDLKEAY DSLCTSGVVR LHINSWLEVS FCLPHKIHYA AS SLIPPEA IERSLKAIRP YHALLLLSDE KSLLGELPID CSPALVRVIK TTSAVKNLQQ LAQDADLALL QVFQLAAHLV YWG KAIIIY PLCENNVYML SPNASVCLYS PLAEQFSHQF PSHDLPSVLA KFSLPVSLSE FRNPLAPAVQ ETQLIQMVVW MLQR RLLIQ LHTYVCLMAS PSEEEPRPRE DDVPFTARVG GRSLSTPNAL SFGSPTSSDD MTLTSPSMDN SSAELLPSGD SPLNQ RMTE NLLASLSEHE RAAILSVPAA QNPEDLRMFA RLLHYFRGRH HLEEIMYNEN TRRSQLLMLF DKFRSVLVVT THEDPV IAV FQALLP

UniProtKB: GATOR1 complex protein NPRL3

-
Macromolecule #3: GATOR1 complex protein DEPDC5

MacromoleculeName: GATOR1 complex protein DEPDC5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 181.478 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRTTKVYKLV IHKKGFGGSD DELVVNPKVF PHIKLGDIVE IAHPNDEYSP LLLQVKSLKE DLQKETISVD QTVTQVFRLR PYQDVYVNV VDPKDVTLDL VELTFKDQYI GRGDMWRLKK SLVSTCAYIT QKVEFAGIRA QAGELWVKNE KVMCGYISED T RVVFRSTS ...String:
MRTTKVYKLV IHKKGFGGSD DELVVNPKVF PHIKLGDIVE IAHPNDEYSP LLLQVKSLKE DLQKETISVD QTVTQVFRLR PYQDVYVNV VDPKDVTLDL VELTFKDQYI GRGDMWRLKK SLVSTCAYIT QKVEFAGIRA QAGELWVKNE KVMCGYISED T RVVFRSTS AMVYIFIQMS CEMWDFDIYG DLYFEKAVNG FLADLFTKWK EKNCSHEVTV VLFSRTFYDA KSVDEFPEIN RA SIRQDHK GRFYEDFYKV VVQNERREEW TSLLVTIKKL FIQYPVLVRL EQAEGFPQGD NSTSAQGNYL EAINLSFNVF DKH YINRNF DRTGQMSVVI TPGVGVFEVD RLLMILTKQR MIDNGIGVDL VCMGEQPLHA VPLFKLHNRS APRDSRLGDD YNIP HWINH SFYTSKSQLF CNSFTPRIKL AGKKPASEKA KNGRDTSLGS PKESENALPI QVDYDAYDAQ VFRLPGPSRA QCLTT CRSV RERESHSRKS ASSCDVSSSP SLPSRTLPTE EVRSQASDDS SLGKSANILM IPHPHLHQYE VSSSLGYTST RDVLEN MME PPQRDSSAPG RFHVGSAESM LHVRPGGYTP QRALINPFAP SRMPMKLTSN RRRWMHTFPV GPSGEAIQIH HQTRQNM AE LQGSGQRDPT HSSAELLELA YHEAAGRHSN SRQPGDGMSF LNFSGTEELS VGLLSNSGAG MNPRTQNKDS LEDSVSTS P DPILTLSAPP VVPGFCCTVG VDWKSLTTPA CLPLTTDYFP DRQGLQNDYT EGCYDLLPEA DIDRRDEDGV QMTAQQVFE EFICQRLMQG YQIIVQPKTQ KPNPAVPPPL SSSPLYSRGL VSRNRPEEED QYWLSMGRTF HKVTLKDKMI TVTRYLPKYP YESAQIHYT YSLCPSHSDS EFVSCWVEFS HERLEEYKWN YLDQYICSAG SEDFSLIESL KFWRTRFLLL PACVTATKRI T EGEAHCDI YGDRPRADED EWQLLDGFVR FVEGLNRIRR RHRSDRMMRK GTAMKGLQMT GPISTHSLES TAPPVGKKGT SA LSALLEM EASQKCLGEQ QAAVHGGKSS AQSAESSSVA MTPTYMDSPR KDGAFFMEFV RSPRTASSAF YPQVSVDQTA TPM LDGTSL GICTGQSMDR GNSQTFGNSQ NIGEQGYSST NSSDSSSQQL VASSLTSSST LTEILEAMKH PSTGVQLLSE QKGL SPYCF ISAEVVHWLV NHVEGIQTQA MAIDIMQKML EEQLITHASG EAWRTFIYGF YFYKIVTDKE PDRVAMQQPA TTWHT AGVD DFASFQRKWF EVAFVAEELV HSEIPAFLLP WLPSRPASYA SRHSSFSRSF GGRSQAAALL AATVPEQRTV TLDVDV NNR TDRLEWCSCY YHGNFSLNAA FEIKLHWMAV TAAVLFEMVQ GWHRKATSCG FLLVPVLEGP FALPSYLYGD PLRAQLF IP LNISCLLKEG SEHLFDSFEP ETYWDRMHLF QEAIAHRFGF VQDKYSASAF NFPAENKPQY IHVTGTVFLQ LPYSKRKF S GQQRRRRNST SSTNQNMFCE ERVGYNWAYN TMLTKTWRSS ATGDEKFADR LLKDFTDFCI NRDNRLVTFW TSCLEKMHA SAP

UniProtKB: GATOR1 complex protein DEPDC5

-
Macromolecule #4: KICSTOR complex protein SZT2

MacromoleculeName: KICSTOR complex protein SZT2 / type: protein_or_peptide / ID: 4 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1 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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7t3b

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 491656
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
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