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- EMDB-35335: Human TRiC-PhLP2A-actin complex in the closed state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35335
TitleHuman TRiC-PhLP2A-actin complex in the closed state
Map data
Sample
  • Complex: Complex of TRiC/CCT, PhLP2A, and actin treated with ATP-AlFx
    • Complex: Human TRiC/CCT complex
      • Protein or peptide: T-complex protein 1 subunit alpha
      • Protein or peptide: T-complex protein 1 subunit beta
      • Protein or peptide: T-complex protein 1 subunit gamma
      • Protein or peptide: T-complex protein 1 subunit delta
      • Protein or peptide: T-complex protein 1 subunit epsilon
      • Protein or peptide: T-complex protein 1 subunit zeta
      • Protein or peptide: T-complex protein 1 subunit eta
      • Protein or peptide: T-complex protein 1 subunit theta
    • Complex: PhLP2A (PDCL3)
      • Protein or peptide: Phosducin-like protein 3
    • Complex: Human actin
      • Protein or peptide: ACTB protein (Fragment)
Keywordschaperonin complex / CHAPERONE / cochaperone
Function / homology
Function and homology information


: / perinucleolar compartment / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / tubulin complex assembly / chaperonin-containing T-complex / : ...: / perinucleolar compartment / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / tubulin complex assembly / chaperonin-containing T-complex / : / BBSome-mediated cargo-targeting to cilium / Formation of tubulin folding intermediates by CCT/TriC / binding of sperm to zona pellucida / Folding of actin by CCT/TriC / vascular endothelial growth factor receptor 2 binding / Prefoldin mediated transfer of substrate to CCT/TriC / RHOBTB1 GTPase cycle / regulation of peptidyl-tyrosine phosphorylation / WD40-repeat domain binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of ubiquitin-dependent protein catabolic process / chaperone-mediated protein complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / RHOBTB2 GTPase cycle / beta-tubulin binding / heterochromatin / : / positive regulation of telomere maintenance via telomerase / positive regulation of endothelial cell proliferation / protein folding chaperone / acrosomal vesicle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA 3'-UTR binding / cell projection / ATP-dependent protein folding chaperone / mRNA 5'-UTR binding / response to virus / positive regulation of angiogenesis / azurophil granule lumen / unfolded protein binding / melanosome / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / protein folding / G-protein beta-subunit binding / cell body / actin cytoskeleton organization / angiogenesis / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cilium / cadherin binding / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / centrosome / positive regulation of gene expression / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / Phosducin, thioredoxin-like domain / Phosducin / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit ...: / Phosducin, thioredoxin-like domain / Phosducin / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
ACTB protein / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit gamma / T-complex protein 1 subunit theta / T-complex protein 1 subunit delta / T-complex protein 1 subunit beta / T-complex protein 1 subunit eta / Phosducin-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.42 Å
AuthorsRoh SH / Park J / Kim H / Lim S
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2024
Title: A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle.
Authors: Junsun Park / Hyunmin Kim / Daniel Gestaut / Seyeon Lim / Kwadwo A Opoku-Nsiah / Alexander Leitner / Judith Frydman / Soung-Hun Roh /
Abstract: Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin- ...Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.
History
DepositionFeb 9, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35335.png

Downloads & links

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Map

FileDownload / File: emd_35335.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.18516637 - 0.41520575
Average (Standard dev.)0.0013465555 (±0.02662727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35335_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_35335_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Complex of TRiC/CCT, PhLP2A, and actin treated with ATP-AlFx

EntireName: Complex of TRiC/CCT, PhLP2A, and actin treated with ATP-AlFx
Components
  • Complex: Complex of TRiC/CCT, PhLP2A, and actin treated with ATP-AlFx
    • Complex: Human TRiC/CCT complex
      • Protein or peptide: T-complex protein 1 subunit alpha
      • Protein or peptide: T-complex protein 1 subunit beta
      • Protein or peptide: T-complex protein 1 subunit gamma
      • Protein or peptide: T-complex protein 1 subunit delta
      • Protein or peptide: T-complex protein 1 subunit epsilon
      • Protein or peptide: T-complex protein 1 subunit zeta
      • Protein or peptide: T-complex protein 1 subunit eta
      • Protein or peptide: T-complex protein 1 subunit theta
    • Complex: PhLP2A (PDCL3)
      • Protein or peptide: Phosducin-like protein 3
    • Complex: Human actin
      • Protein or peptide: ACTB protein (Fragment)

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Supramolecule #1: Complex of TRiC/CCT, PhLP2A, and actin treated with ATP-AlFx

SupramoleculeName: Complex of TRiC/CCT, PhLP2A, and actin treated with ATP-AlFx
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1 MDa

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Supramolecule #2: Human TRiC/CCT complex

SupramoleculeName: Human TRiC/CCT complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: PhLP2A (PDCL3)

SupramoleculeName: PhLP2A (PDCL3) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Human actin

SupramoleculeName: Human actin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #10
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: T-complex protein 1 subunit alpha

MacromoleculeName: T-complex protein 1 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.418477 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEGPLSVFGD RSTGETIRSQ NVMAAASIAN IVKSSLGPVG LDKMLVDDIG DVTITNDGAT ILKLLEVEHP AAKVLCELAD LQDKEVGDG TTSVVIIAAE LLKNADELVK QKIHPTSVIS GYRLACKEAV RYINENLIVN TDELGRDCLI NAAKTSMSSK I IGINGDFF ...String:
MEGPLSVFGD RSTGETIRSQ NVMAAASIAN IVKSSLGPVG LDKMLVDDIG DVTITNDGAT ILKLLEVEHP AAKVLCELAD LQDKEVGDG TTSVVIIAAE LLKNADELVK QKIHPTSVIS GYRLACKEAV RYINENLIVN TDELGRDCLI NAAKTSMSSK I IGINGDFF ANMVVDAVLA IKYTDIRGQP RYPVNSVNIL KAHGRSQMES MLISGYALNC VVGSQGMPKR IVNAKIACLD FS LQKTKMK LGVQVVITDP EKLDQIRQRE SDITKERIQK ILATGANVIL TTGGIDDMCL KYFVEAGAMA VRRVLKRDLK RIA KASGAT ILSTLANLEG EETFEAAMLG QAEEVVQERI CDDELILIKN TKARTSASII LRGANDFMCD EMERSLHDAL CVVK RVLES KSVVPGGGAV EAALSIYLEN YATSMGSREQ LAIAEFARSL LVIPNTLAVN AAQDSTDLVA KLRAFHNEAQ VNPER KNLK WIGLDLSNGK PRDNKQAGVF EPTIVKVKSL KFATEAAITI LRIDDLIKLH PESKDDKHGS YEDAVHSGAL ND

UniProtKB: T-complex protein 1 subunit alpha

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Macromolecule #2: T-complex protein 1 subunit beta

MacromoleculeName: T-complex protein 1 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.567141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASLSLAPVN IFKAGADEER AETARLTSFI GAIAIGDLVK STLGPKGMDK ILLSSGRDAS LMVTNDGATI LKNIGVDNPA AKVLVDMSR VQDDEVGDGT TSVTVLAAEL LREAESLIAK KIHPQTIIAG WREATKAARE ALLSSAVDHG SDEVKFRQDL M NIAGTTLS ...String:
MASLSLAPVN IFKAGADEER AETARLTSFI GAIAIGDLVK STLGPKGMDK ILLSSGRDAS LMVTNDGATI LKNIGVDNPA AKVLVDMSR VQDDEVGDGT TSVTVLAAEL LREAESLIAK KIHPQTIIAG WREATKAARE ALLSSAVDHG SDEVKFRQDL M NIAGTTLS SKLLTHHKDH FTKLAVEAVL RLKGSGNLEA IHIIKKLGGS LADSYLDEGF LLDKKIGVNQ PKRIENAKIL IA NTGMDTD KIKIFGSRVR VDSTAKVAEI EHAEKEKMKE KVERILKHGI NCFINRQLIY NYPEQLFGAA GVMAIEHADF AGV ERLALV TGGEIASTFD HPELVKLGSC KLIEEVMIGE DKLIHFSGVA LGEACTIVLR GATQQILDEA ERSLHDALCV LAQT VKDSR TVYGGGCSEM LMAHAVTQLA NRTPGKEAVA MESYAKALRM LPTIIADNAG YDSADLVAQL RAAHSEGNTT AGLDM REGT IGDMAILGIT ESFQVKRQVL LSAAEAAEVI LRVDNIIKAA PRKRVPDHHP C

UniProtKB: T-complex protein 1 subunit beta

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Macromolecule #3: T-complex protein 1 subunit gamma

MacromoleculeName: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.613855 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MMGHRPVLVL SQNTKRESGR KVQSGNINAA KTIADIIRTC LGPKSMMKML LDPMGGIVMT NDGNAILREI QVQHPAAKSM IEISRTQDE EVGDGTTSVI ILAGEMLSVA EHFLEQQMHP TVVISAYRKA LDDMISTLKK ISIPVDISDS DMMLNIINSS I TTKAISRW ...String:
MMGHRPVLVL SQNTKRESGR KVQSGNINAA KTIADIIRTC LGPKSMMKML LDPMGGIVMT NDGNAILREI QVQHPAAKSM IEISRTQDE EVGDGTTSVI ILAGEMLSVA EHFLEQQMHP TVVISAYRKA LDDMISTLKK ISIPVDISDS DMMLNIINSS I TTKAISRW SSLACNIALD AVKMVQFEEN GRKEIDIKKY ARVEKIPGGI IEDSCVLRGV MINKDVTHPR MRRYIKNPRI VL LDSSLEY KKGESQTDIE ITREEDFTRI LQMEEEYIQQ LCEDIIQLKP DVVITEKGIS DLAQHYLMRA NITAIRRVRK TDN NRIARA CGARIVSRPE ELREDDVGTG AGLLEIKKIG DEYFTFITDC KDPKACTILL RGASKEILSE VERNLQDAMQ VCRN VLLDP QLVPGGGASE MAVAHALTEK SKAMTGVEQW PYRAVAQALE VIPRTLIQNC GASTIRLLTS LRAKHTQENC ETWGV NGET GTLVDMKELG IWEPLAVKLQ TYKTAVETAV LLLRIDDIVS GHKKKGDDQS RQGGAPDAGQ E

UniProtKB: T-complex protein 1 subunit gamma

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Macromolecule #4: T-complex protein 1 subunit delta

MacromoleculeName: T-complex protein 1 subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.996113 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPENVAPRSG ATAGAAGGRG KGAYQDRDKP AQIRFSNISA AKAVADAIRT SLGPKGMDKM IQDGKGDVTI TNDGATILKQ MQVLHPAAR MLVELSKAQD IEAGDGTTSV VIIAGSLLDS CTKLLQKGIH PTIISESFQK ALEKGIEILT DMSRPVELSD R ETLLNSAT ...String:
MPENVAPRSG ATAGAAGGRG KGAYQDRDKP AQIRFSNISA AKAVADAIRT SLGPKGMDKM IQDGKGDVTI TNDGATILKQ MQVLHPAAR MLVELSKAQD IEAGDGTTSV VIIAGSLLDS CTKLLQKGIH PTIISESFQK ALEKGIEILT DMSRPVELSD R ETLLNSAT TSLNSKVVSQ YSSLLSPMSV NAVMKVIDPA TATSVDLRDI KIVKKLGGTI DDCELVEGLV LTQKVSNSGI TR VEKAKIG LIQFCLSAPK TDMDNQIVVS DYAQMDRVLR EERAYILNLV KQIKKTGCNV LLIQKSILRD ALSDLALHFL NKM KIMVIK DIEREDIEFI CKTIGTKPVA HIDQFTADML GSAELAEEVN LNGSGKLLKI TGCASPGKTV TIVVRGSNKL VIEE AERSI HDALCVIRCL VKKRALIAGG GAPEIELALR LTEYSRTLSG MESYCVRAFA DAMEVIPSTL AENAGLNPIS TVTEL RNRH AQGEKTAGIN VRKGGISNIL EELVVQPLLV SVSALTLATE TVRSILKIDD VVNTR

UniProtKB: T-complex protein 1 subunit delta

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Macromolecule #5: T-complex protein 1 subunit epsilon

MacromoleculeName: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.749957 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASMGTLAFD EYGRPFLIIK DQDRKSRLMG LEALKSHIMA AKAVANTMRT SLGPNGLDKM MVDKDGDVTV TNDGATILSM MDVDHQIAK LMVELSKSQD DEIGDGTTGV VVLAGALLEE AEQLLDRGIH PIRIADGYEQ AARVAIEHLD KISDSVLVDI K DTEPLIQT ...String:
MASMGTLAFD EYGRPFLIIK DQDRKSRLMG LEALKSHIMA AKAVANTMRT SLGPNGLDKM MVDKDGDVTV TNDGATILSM MDVDHQIAK LMVELSKSQD DEIGDGTTGV VVLAGALLEE AEQLLDRGIH PIRIADGYEQ AARVAIEHLD KISDSVLVDI K DTEPLIQT AKTTLGSKVV NSCHRQMAEI AVNAVLTVAD MERRDVDFEL IKVEGKVGGR LEDTKLIKGV IVDKDFSHPQ MP KKVEDAK IAILTCPFEP PKPKTKHKLD VTSVEDYKAL QKYEKEKFEE MIQQIKETGA NLAICQWGFD DEANHLLLQN NLP AVRWVG GPEIELIAIA TGGRIVPRFS ELTAEKLGFA GLVQEISFGT TKDKMLVIEQ CKNSRAVTIF IRGGNKMIIE EAKR SLHDA LCVIRNLIRD NRVVYGGGAA EISCALAVSQ EADKCPTLEQ YAMRAFADAL EVIPMALSEN SGMNPIQTMT EVRAR QVKE MNPALGIDCL HKGTNDMKQQ HVIETLIGKK QQISLATQMV RMILKIDDIR KPGESEE

UniProtKB: T-complex protein 1 subunit epsilon

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Macromolecule #6: T-complex protein 1 subunit zeta

MacromoleculeName: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.106086 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAVKTLNPK AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQIQ HPTASLIAKV ATAQDDITG DGTTSNVLII GELLKQADLY ISEGLHPRII TEGFEAAKEK ALQFLEEVKV SREMDRETLI DVARTSLRTK V HAELADVL ...String:
MAAVKTLNPK AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQIQ HPTASLIAKV ATAQDDITG DGTTSNVLII GELLKQADLY ISEGLHPRII TEGFEAAKEK ALQFLEEVKV SREMDRETLI DVARTSLRTK V HAELADVL TEAVVDSILA IKKQDEPIDL FMIEIMEMKH KSETDTSLIR GLVLDHGARH PDMKKRVEDA YILTCNVSLE YE KTEVNSG FFYKSAEERE KLVKAERKFI EDRVKKIIEL KRKVCGDSDK GFVVINQKGI DPFSLDALSK EGIVALRRAK RRN MERLTL ACGGVALNSF DDLSPDCLGH AGLVYEYTLG EEKFTFIEKC NNPRSVTLLI KGPNKHTLTQ IKDAVRDGLR AVKN AIDDG CVVPGAGAVE VAMAEALIKH KPSVKGRAQL GVQAFADALL IIPKVLAQNS GFDLQETLVK IQAEHSESGQ LVGVD LNTG EPMVAAEVGV WDNYCVKKQL LHSCTVIATN ILLVDEIMRA GMSSLKG

UniProtKB: T-complex protein 1 subunit zeta

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Macromolecule #7: T-complex protein 1 subunit eta

MacromoleculeName: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.443535 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MMPTPVILLK EGTDSSQGIP QLVSNISACQ VIAEAVRTTL GPRGMDKLIV DGRGKATISN DGATILKLLD VVHPAAKTLV DIAKSQDAE VGDGTTSVTL LAAEFLKQVK PYVEEGLHPQ IIIRAFRTAT QLAVNKIKEI AVTVKKADKV EQRKLLEKCA M TALSSKLI ...String:
MMPTPVILLK EGTDSSQGIP QLVSNISACQ VIAEAVRTTL GPRGMDKLIV DGRGKATISN DGATILKLLD VVHPAAKTLV DIAKSQDAE VGDGTTSVTL LAAEFLKQVK PYVEEGLHPQ IIIRAFRTAT QLAVNKIKEI AVTVKKADKV EQRKLLEKCA M TALSSKLI SQQKAFFAKM VVDAVMMLDD LLQLKMIGIK KVQGGALEDS QLVAGVAFKK TFSYAGFEMQ PKKYHNPKIA LL NVELELK AEKDNAEIRV HTVEDYQAIV DAEWNILYDK LEKIHHSGAK VVLSKLPIGD VATQYFADRD MFCAGRVPEE DLK RTMMAC GGSIQTSVNA LSADVLGRCQ VFEETQIGGE RYNFFTGCPK AKTCTFILRG GAEQFMEETE RSLHDAIMIV RRAI KNDSV VAGGGAIEME LSKYLRDYSR TIPGKQQLLI GAYAKALEII PRQLCDNAGF DATNILNKLR ARHAQGGTWY GVDIN NEDI ADNFEAFVWE PAMVRINALT AASEAACLIV SVDETIKNPR STVDAPTAAG RGRGRGRPH

UniProtKB: T-complex protein 1 subunit eta

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Macromolecule #8: T-complex protein 1 subunit theta

MacromoleculeName: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.691422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MALHVPKAPG FAQMLKEGAK HFSGLEEAVY RNIQACKELA QTTRTAYGPN GMNKMVINHL EKLFVTNDAA TILRELEVQH PAAKMIVMA SHMQEQEVGD GTNFVLVFAG ALLELAEELL RIGLSVSEVI EGYEIACRKA HEILPNLVCC SAKNLRDIDE V SSLLRTSI ...String:
MALHVPKAPG FAQMLKEGAK HFSGLEEAVY RNIQACKELA QTTRTAYGPN GMNKMVINHL EKLFVTNDAA TILRELEVQH PAAKMIVMA SHMQEQEVGD GTNFVLVFAG ALLELAEELL RIGLSVSEVI EGYEIACRKA HEILPNLVCC SAKNLRDIDE V SSLLRTSI MSKQYGNEVF LAKLIAQACV SIFPDSGHFN VDNIRVCKIL GSGISSSSVL HGMVFKKETE GDVTSVKDAK IA VYSCPFD GMITETKGTV LIKTAEELMN FSKGEENLMD AQVKAIADTG ANVVVTGGKV ADMALHYANK YNIMLVRLNS KWD LRRLCK TVGATALPRL TPPVLEEMGH CDSVYLSEVG DTQVVVFKHE KEDGAISTIV LRGSTDNLMD DIERAVDDGV NTFK VLTRD KRLVPGGGAT EIELAKQITS YGETCPGLEQ YAIKKFAEAF EAIPRALAEN SGVKANEVIS KLYAVHQEGN KNVGL DIEA EVPAVKDMLE AGILDTYLGK YWAIKLATNA AVTVLRVDQI IMAKPAGGPK PPSGKKDWDD DQND

UniProtKB: T-complex protein 1 subunit theta

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Macromolecule #9: Phosducin-like protein 3

MacromoleculeName: Phosducin-like protein 3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.650383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQDPNADTEW NDILRKKGIL PPKESLKELE EEAEEEQRIL QQSVVKTYED MTLEELEDHE DEFNEEDERA IEMYRRRRLA EWKATKLKN KFGEVLEISG KDYVQEVTKA GEGLWVILHL YKQGIPLCAL INQHLSGLAR KFPDVKFIKA ISTTCIPNYP D RNLPTIFV ...String:
MQDPNADTEW NDILRKKGIL PPKESLKELE EEAEEEQRIL QQSVVKTYED MTLEELEDHE DEFNEEDERA IEMYRRRRLA EWKATKLKN KFGEVLEISG KDYVQEVTKA GEGLWVILHL YKQGIPLCAL INQHLSGLAR KFPDVKFIKA ISTTCIPNYP D RNLPTIFV YLEGDIKAQF IGPLVFGGMN LTRDELEWKL SESGAIMTDL EENPKKPIED VLLSSVRRSV LMKRDSDSEG D

UniProtKB: Phosducin-like protein 3

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Macromolecule #10: ACTB protein (Fragment)

MacromoleculeName: ACTB protein (Fragment) / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.78266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: ACTB protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 3635 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1821423
Details: The initial particle selection after 2D class classification
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2 prediction model / Details: The model of PhLP2A was built using Colabfold 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 8378
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 5 / Avg.num./class: 20000 / Software - Name: cryoSPARC (ver. 3.2.0) / Details: The final 3D classification
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7nvm


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ib8:
Human TRiC-PhLP2A-actin complex in the closed state

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