[English] 日本語
Yorodumi
- EMDB-64902: Cryo-EM structure of human full length KICSTOR complex (state 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64902
TitleCryo-EM structure of human full length KICSTOR complex (state 2)
Map datafull map
Sample
  • Complex: Structure of KICSTOR complex
    • Protein or peptide: KICSTOR complex protein SZT2
    • Protein or peptide: KICSTOR complex protein ITFG2
    • Protein or peptide: KICSTOR complex protein kaptin
    • Protein or peptide: KICSTOR subunit 2
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 / intercellular bridge / 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 / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
KICSTOR subunit 2 / KICSTOR complex protein C12orf66-like, central domain superfamily / KICSTOR complex C12orf66 like / 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 subunit 2 / KICSTOR complex protein kaptin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSu M-Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other government20231120103446003 China
CitationJournal: To Be Published
Title: Structure of KICSTOR complex
Authors: Su M-Y
History
DepositionJun 3, 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_64902.png

Downloads & links

-
Map

FileDownload / File: emd_64902.map.gz / Format: CCP4 / Size: 1.4 GB / 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 720 pix.
= 612. Å		0.85 Å/pix.
x 720 pix.
= 612. Å		0.85 Å/pix.
x 720 pix.
= 612. 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: 0.0718
Minimum - Maximum-0.603923 - 1.8603233
Average (Standard dev.)-0.00064248237 (±0.0171027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 612.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64902_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: mask for local refinement on SZ1-SZ2-SZ3 region

Fileemd_64902_additional_1.map
Annotationmask for local refinement on SZ1-SZ2-SZ3 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: mask for local refinement on SZ7-C12orf66 region

Fileemd_64902_additional_2.map
Annotationmask for local refinement on SZ7-C12orf66 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: local refined map on SZ7-C12orf66 region

Fileemd_64902_additional_3.map
Annotationlocal refined map on SZ7-C12orf66 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: local refined map on SZ1-SZ2-SZ3 region

Fileemd_64902_additional_4.map
Annotationlocal refined map on SZ1-SZ2-SZ3 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_64902_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_64902_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of KICSTOR complex

EntireName: Structure of KICSTOR complex
Components
  • Complex: Structure of KICSTOR complex
    • Protein or peptide: KICSTOR complex protein SZT2
    • Protein or peptide: KICSTOR complex protein ITFG2
    • Protein or peptide: KICSTOR complex protein kaptin
    • Protein or peptide: KICSTOR subunit 2

-
Supramolecule #1: Structure of KICSTOR complex

SupramoleculeName: Structure of KICSTOR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 525 KDa

-
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

-
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

-
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

-
Macromolecule #4: KICSTOR subunit 2

MacromoleculeName: KICSTOR subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.469758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGESIPLAAP VPVEQAVLET FFSHLGIFSY DKAKDNVEKE REANKSAGGS WLSLLAALAH LAAAEKVYHS LTYLGQKLGG QSFFSRKDS IRTIYTSLHN ELKKVVTGRG ALGGTAPHVE ELLSHLSEQL CFFVQARMEI ADFYEKMYTL STQKFINAEE L VGLLDAIM ...String:
MGESIPLAAP VPVEQAVLET FFSHLGIFSY DKAKDNVEKE REANKSAGGS WLSLLAALAH LAAAEKVYHS LTYLGQKLGG QSFFSRKDS IRTIYTSLHN ELKKVVTGRG ALGGTAPHVE ELLSHLSEQL CFFVQARMEI ADFYEKMYTL STQKFINAEE L VGLLDAIM KKYSSRFHHP ILSPLESSFQ LEVDVLCHLL KAQAQVSEWK FLPSLVNLHS AHTKLQTWGQ IFEKQRETKK HL FGGQSQK AVQPPHLFLW LMKLKNMLLA KFSFYFHEAL SRQTTASEMK TLTAKANPDF FGKISSFIRK YDAANVSLIF DNR GSESFQ GHGYHHPHSY REAPKGVDQY PAVVSLPSDR PVMHWPNVIM IMTDRTSDLN SLEKVVHFYD DKVQSTYFLT RPEP HFTIV IIFESKKSER DSHFISFLNE VSLALKNPKV FASLKPGAKG

UniProtKB: KICSTOR subunit 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.74 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

-
Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.88 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

-
Electron microscopy #1~~

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 3 / Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

-
Electron microscopy #1~~~

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 4 / Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.61 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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 #1

Image processing ID1
Image recording ID1
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280444
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
Image processing #2

Image processing ID2
Image recording ID2
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold model
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
Image processing #3

Image processing ID3
Image recording ID3
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold model
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
Image processing #4

Image processing ID4
Image recording ID4
CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold model
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