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Yorodumi- EMDB-13754: Human TRiC complex in open state with nanobody bound (map-only) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13754 | |||||||||
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Title | Human TRiC complex in open state with nanobody bound (map-only) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Kelly JJ / Chi G / Bulawa C / Paavilainen VO / Bountra C / Huiskonen JT / Yue W | |||||||||
Funding support | Finland, 2 items
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Citation | Journal: To Be Published Title: Human TRiC complex in open state with nanobody bound (map-only) Authors: Kelly JJ / Chi G / Bulawa C / Paavilainen VO / Bountra C / Huiskonen JT / Yue W | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13754.map.gz | 227.3 MB | EMDB map data format | |
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Header (meta data) | emd-13754-v30.xml emd-13754.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13754_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_13754.png | 169.8 KB | ||
Masks | emd_13754_msk_1.map | 244.1 MB | Mask map | |
Others | emd_13754_half_map_1.map.gz emd_13754_half_map_2.map.gz | 194.5 MB 194.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13754 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13754 | HTTPS FTP |
-Validation report
Summary document | emd_13754_validation.pdf.gz | 544 KB | Display | EMDB validaton report |
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Full document | emd_13754_full_validation.pdf.gz | 543.5 KB | Display | |
Data in XML | emd_13754_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_13754_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13754 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13754 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13754.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13754_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13754_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13754_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human type II chaperonin TRiC/CCT complex with nanobody bound
Entire | Name: Human type II chaperonin TRiC/CCT complex with nanobody bound |
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Components |
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-Supramolecule #1: Human type II chaperonin TRiC/CCT complex with nanobody bound
Supramolecule | Name: Human type II chaperonin TRiC/CCT complex with nanobody bound type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: T-complex protein 1 subunit epsilon
Macromolecule | Name: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MASMGTLAFD EYGRPFLIIK DQDRKSRLMG LEALKSHIMA AKAVANTMRT SLGPNGLDKM MVDKDGDVT VTNDGATILS MMDVDHQIAK LMVELSKSQD DEIGDGTTGV VVLAGALLEE A EQLLDRGI HPIRIADGYE QAARVAIEHL DKISDSVLVD IKDTEPLIQT ...String: MASMGTLAFD EYGRPFLIIK DQDRKSRLMG LEALKSHIMA AKAVANTMRT SLGPNGLDKM MVDKDGDVT VTNDGATILS MMDVDHQIAK LMVELSKSQD DEIGDGTTGV VVLAGALLEE A EQLLDRGI HPIRIADGYE QAARVAIEHL DKISDSVLVD IKDTEPLIQT AKTTLGSKVV NS CHRQMAE IAVNAVLTVA DMERRDVDFE LIKVEGKVGG RLEDTKLIKG VIVDKDFSHP QMP KKVEDA KIAILTCPFE PPKPKTKHKL DVTSVEDYKA LQKYEKEKFE EMIQQIKETG ANLA ICQWG FDDEANHLLL QNNLPAVRWV GGPEIELIAI ATGGRIVPRF SELTAEKLGF AGLVQ EISF GTTKDKMLVI EQCKNSRAVT IFIRGGNKMI IEEAKRSLHD ALCVIRNLIR DNRVVY GGG AAEISCALAV SQEADKCPTL EQYAMRAFAD ALEVIPMALS ENSGMNPIQT MTEVRAR QV KEMNPALGID CLHKGTNDMK QQHVIETLIG KKQQISLATQ MVRMILKIDD IRKPGESE E |
-Macromolecule #2: T-complex protein 1 subunit eta
Macromolecule | Name: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MMPTPVILLK EGTDSSQGIP QLVSNISACQ VIAEAVRTTL GPRGMDKLIV DGRGKATISN DGATILKLL DVVHPAAKTL VDIAKSQDAE VGDGTTSVTL LAAEFLKQVK PYVEEGLHPQ I IIRAFRTA TQLAVNKIKE IAVTVKKADK VEQRKLLEKC AMTALSSKLI ...String: MMPTPVILLK EGTDSSQGIP QLVSNISACQ VIAEAVRTTL GPRGMDKLIV DGRGKATISN DGATILKLL DVVHPAAKTL VDIAKSQDAE VGDGTTSVTL LAAEFLKQVK PYVEEGLHPQ I IIRAFRTA TQLAVNKIKE IAVTVKKADK VEQRKLLEKC AMTALSSKLI SQQKAFFAKM VV DAVMMLD DLLQLKMIGI KKVQGGALED SQLVAGVAFK KTFSYAGFEM QPKKYHNPKI ALL NVELEL KAEKDNAEIR VHTVEDYQAI VDAEWNILYD KLEKIHHSGA KVVLSKLPIG DVAT QYFAD RDMFCAGRVP EEDLKRTMMA CGGSIQTSVN ALSADVLGRC QVFEETQIGG ERYNF FTGC PKAKTCTFIL RGGAEQFMEE TERSLHDAIM IVRRAIKNDS VVAGGGAIEM ELSKYL RDY SRTIPGKQQL LIGAYAKALE IIPRQLCDNA GFDATNILNK LRARHAQGGT WYGVDIN NE DIADNFEAFV WEPAMVRINA LTAASEAACL IVSVDETIKN PRSTVDAPTA AGRGRGRG R PH |
-Macromolecule #3: T-complex protein 1 subunit theta
Macromolecule | Name: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MALHVPKAPG FAQMLKEGAK HFSGLEEAVY RNIQACKELA QTTRTAYGPN GMNKMVINHL EKLFVTNDA ATILRELEVQ HPAAKMIVMA SHMQEQEVGD GTNFVLVFAG ALLELAEELL R IGLSVSEV IEGYEIACRK AHEILPNLVC CSAKNLRDID EVSSLLRTSI ...String: MALHVPKAPG FAQMLKEGAK HFSGLEEAVY RNIQACKELA QTTRTAYGPN GMNKMVINHL EKLFVTNDA ATILRELEVQ HPAAKMIVMA SHMQEQEVGD GTNFVLVFAG ALLELAEELL R IGLSVSEV IEGYEIACRK AHEILPNLVC CSAKNLRDID EVSSLLRTSI MSKQYGNEVF LA KLIAQAC VSIFPDSGHF NVDNIRVCKI LGSGISSSSV LHGMVFKKET EGDVTSVKDA KIA VYSCPF DGMITETKGT VLIKTAEELM NFSKGEENLM DAQVKAIADT GANVVVTGGK VADM ALHYA NKYNIMLVRL NSKWDLRRLC KTVGATALPR LTPPVLEEMG HCDSVYLSEV GDTQV VVFK HEKEDGAIST IVLRGSTDNL MDDIERAVDD GVNTFKVLTR DKRLVPGGGA TEIELA KQI TSYGETCPGL EQYAIKKFAE AFEAIPRALA ENSGVKANEV ISKLYAVHQE GNKNVGL DI EAEVPAVKDM LEAGILDTYL GKYWAIKLAT NAAVTVLRVD QIIMAKPAGG PKPPSGKK D WDDDQND |
-Macromolecule #4: T-complex protein 1 subunit zeta
Macromolecule | Name: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MAAVKTLNPK AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQI QHPTASLIAK VATAQDDITG DGTTSNVLII GELLKQADLY ISEGLHPRII T EGFEAAKE KALQFLEEVK VSREMDRETL IDVARTSLRT KVHAELADVL ...String: MAAVKTLNPK AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQI QHPTASLIAK VATAQDDITG DGTTSNVLII GELLKQADLY ISEGLHPRII T EGFEAAKE KALQFLEEVK VSREMDRETL IDVARTSLRT KVHAELADVL TEAVVDSILA IK KQDEPID LFMIEIMEMK HKSETDTSLI RGLVLDHGAR HPDMKKRVED AYILTCNVSL EYE KTEVNS GFFYKSAEER EKLVKAERKF IEDRVKKIIE LKRKVCGDSD KGFVVINQKG IDPF SLDAL SKEGIVALRR AKRRNMERLT LACGGVALNS FDDLSPDCLG HAGLVYEYTL GEEKF TFIE KCNNPRSVTL LIKGPNKHTL TQIKDAVRDG LRAVKNAIDD GCVVPGAGAV EVAMAE ALI KHKPSVKGRA QLGVQAFADA LLIIPKVLAQ NSGFDLQETL VKIQAEHSES GQLVGVD LN TGEPMVAAEV GVWDNYCVKK QLLHSCTVIA TNILLVDEIM RAGMSSLKG |
-Macromolecule #5: T-complex protein 1 subunit gamma
Macromolecule | Name: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MMGHRPVLVL SQNTKRESGR KVQSGNINAA KTIADIIRTC LGPKSMMKML LDPMGGIVMT NDGNAILRE IQVQHPAAKS MIEISRTQDE EVGDGTTSVI ILAGEMLSVA EHFLEQQMHP T VVISAYRK ALDDMISTLK KISIPVDISD SDMMLNIINS SITTKAISRW ...String: MMGHRPVLVL SQNTKRESGR KVQSGNINAA KTIADIIRTC LGPKSMMKML LDPMGGIVMT NDGNAILRE IQVQHPAAKS MIEISRTQDE EVGDGTTSVI ILAGEMLSVA EHFLEQQMHP T VVISAYRK ALDDMISTLK KISIPVDISD SDMMLNIINS SITTKAISRW SSLACNIALD AV KMVQFEE NGRKEIDIKK YARVEKIPGG IIEDSCVLRG VMINKDVTHP RMRRYIKNPR IVL LDSSLE YKKGESQTDI EITREEDFTR ILQMEEEYIQ QLCEDIIQLK PDVVITEKGI SDLA QHYLM RANITAIRRV RKTDNNRIAR ACGARIVSRP EELREDDVGT GAGLLEIKKI GDEYF TFIT DCKDPKACTI LLRGASKEIL SEVERNLQDA MQVCRNVLLD PQLVPGGGAS EMAVAH ALT EKSKAMTGVE QWPYRAVAQA LEVIPRTLIQ NCGASTIRLL TSLRAKHTQE NCETWGV NG ETGTLVDMKE LGIWEPLAVK LQTYKTAVET AVLLLRIDDI VSGHKKKGDD QSRQGGAP D AGQE |
-Macromolecule #6: T-complex 1 subunit alpha
Macromolecule | Name: T-complex 1 subunit alpha / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MEGPLSVFGD RSTGETIRSQ NVMAAASIAN IVKSSLGPVG LDKMLVDDIG DVTITNDGAT ILKLLEVEH PAAKVLCELA DLQDKEVGDG TTSVVIIAAE LLKNADELVK QKIHPTSVIS G YRLACKEA VRYINENLIV NTDELGRDCL INAAKTSMSS KIIGINGDFF ...String: MEGPLSVFGD RSTGETIRSQ NVMAAASIAN IVKSSLGPVG LDKMLVDDIG DVTITNDGAT ILKLLEVEH PAAKVLCELA DLQDKEVGDG TTSVVIIAAE LLKNADELVK QKIHPTSVIS G YRLACKEA VRYINENLIV NTDELGRDCL INAAKTSMSS KIIGINGDFF ANMVVDAVLA IK YTDIRGQ PRYPVNSVNI LKAHGRSQME SMLISGYALN CVVGSQGMPK RIVNAKIACL DFS LQKTKM KLGVQVVITD PEKLDQIRQR ESDITKERIQ KILATGANVI LTTGGIDDMC LKYF VEAGA MAVRRVLKRD LKRIAKASGA TILSTLANLE GEETFEAAML GQAEEVVQER ICDDE LILI KNTKARTSAS IILRGANDFM CDEMERSLHD ALCVVKRVLE SKSVVPGGGA VEAALS IYL ENYATSMGSR EQLAIAEFAR SLLVIPNTLA VNAAQDSTDL VAKLRAFHNE AQVNPER KN LKWIGLDLSN GKPRDNKQAG VFEPTIVKVK SLKFATEAAI TILRIDDLIK LHPESKDD K HGSYEDAVHS GALND |
-Macromolecule #7: T-complex 1 subunit delta
Macromolecule | Name: T-complex 1 subunit delta / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MPENVAPRSG ATAGAAGGRG KGAYQDRDKP AQIRFSNISA AKAVADAIRT SLGPKGMDKM IQDGKGDVT ITNDGATILK QMQVLHPAAR MLVELSKAQD IEAGDGTTSV VIIAGSLLDS C TKLLQKGI HPTIISESFQ KALEKGIEIL TDMSRPVELS DRETLLNSAT ...String: MPENVAPRSG ATAGAAGGRG KGAYQDRDKP AQIRFSNISA AKAVADAIRT SLGPKGMDKM IQDGKGDVT ITNDGATILK QMQVLHPAAR MLVELSKAQD IEAGDGTTSV VIIAGSLLDS C TKLLQKGI HPTIISESFQ KALEKGIEIL TDMSRPVELS DRETLLNSAT TSLNSKVVSQ YS SLLSPMS VNAVMKVIDP ATATSVDLRD IKIVKKLGGT IDDCELVEGL VLTQKVSNSG ITR VEKAKI GLIQFCLSAP KTDMDNQIVV SDYAQMDRVL REERAYILNL VKQIKKTGCN VLLI QKSIL RDALSDLALH FLNKMKIMVI KDIEREDIEF ICKTIGTKPV AHIDQFTADM LGSAE LAEE VNLNGSGKLL KITGCASPGK TVTIVVRGSN KLVIEEAERS IHDALCVIRC LVKKRA LIA GGGAPEIELA LRLTEYSRTL SGMESYCVRA FADAMEVIPS TLAENAGLNP ISTVTEL RN RHAQGEKTAG INVRKGGISN ILEELVVQPL LVSVSALTLA TETVRSILKI DDVVNTR |
-Macromolecule #8: T-complex 1 subunit beta
Macromolecule | Name: T-complex 1 subunit beta / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MASLSLAPVN IFKAGADEER AETARLTSFI GAIAIGDLVK STLGPKGMDK ILLSSGRDAS LMVTNDGAT ILKNIGVDNP AAKVLVDMSR VQDDEVGDGT TSVTVLAAEL LREAESLIAK K IHPQTIIA GWREATKAAR EALLSSAVDH GSDEVKFRQD LMNIAGTTLS ...String: MASLSLAPVN IFKAGADEER AETARLTSFI GAIAIGDLVK STLGPKGMDK ILLSSGRDAS LMVTNDGAT ILKNIGVDNP AAKVLVDMSR VQDDEVGDGT TSVTVLAAEL LREAESLIAK K IHPQTIIA GWREATKAAR EALLSSAVDH GSDEVKFRQD LMNIAGTTLS SKLLTHHKDH FT KLAVEAV LRLKGSGNLE AIHIIKKLGG SLADSYLDEG FLLDKKIGVN QPKRIENAKI LIA NTGMDT DKIKIFGSRV RVDSTAKVAE IEHAEKEKMK EKVERILKHG INCFINRQLI YNYP EQLFG AAGVMAIEHA DFAGVERLAL VTGGEIASTF DHPELVKLGS CKLIEEVMIG EDKLI HFSG VALGEACTIV LRGATQQILD EAERSLHDAL CVLAQTVKDS RTVYGGGCSE MLMAHA VTQ LANRTPGKEA VAMESYAKAL RMLPTIIADN AGYDSADLVA QLRAAHSEGN TTAGLDM RE GTIGDMAILG ITESFQVKRQ VLLSAAEAAE VILRVDNIIK AAPRKRVPDH HPC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |