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- EMDB-4169: N terminal region of dynein tail domains in complex with dynactin... -

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Basic information

Entry
Database: EMDB / ID: EMD-4169
TitleN terminal region of dynein tail domains in complex with dynactin filament and BICDR-1
Map dataMap of the N-terminal half of two dynein tail domains bound to dynactin and BICDR1. This map was generated after particle signal subtraction from the overall map (separate deposition)
Sample
  • Complex: Two dynein tail domains bound to dynactin and BICDR1.
    • Complex: dynactin filament
      • Protein or peptide: ARP1 actin related protein 1 homolog A
      • Protein or peptide: Capping protein (Actin filament) muscle Z-line, alpha 1
      • Protein or peptide: F-actin capping protein beta subunit
      • Protein or peptide: Dynactin subunit 2
      • Protein or peptide: Dynactin subunit 2
    • Complex: Cytoplasmic dynein
      • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
      • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Complex: BICDR1
      • Protein or peptide: BICD family-like cargo adapter 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCryo-EM / Complex / MOTOR PROTEIN / Cargo adaptor
Function / homology
Function and homology information


Golgi to secretory granule transport / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / RHOF GTPase cycle / dynactin complex / transport along microtubule / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane ...Golgi to secretory granule transport / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / RHOF GTPase cycle / dynactin complex / transport along microtubule / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex / WASH complex / Recruitment of mitotic centrosome proteins and complexes / dynein light chain binding / dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / barbed-end actin filament capping / establishment of spindle localization / regulation of cell morphogenesis / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule motor activity / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / COPI-mediated anterograde transport / microtubule-based movement / nuclear migration / cortical cytoskeleton / dynein intermediate chain binding / dynactin binding / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / cytoskeleton organization / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / stress granule assembly / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / regulation of mitotic spindle organization / AURKA Activation by TPX2 / sarcomere / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / small GTPase binding / neuron projection development / HCMV Early Events / Aggrephagy / actin filament binding / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cold-induced thermogenesis / actin binding / actin cytoskeleton organization / cell cortex / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
: / Dynamitin / Dynamitin / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. ...: / Dynamitin / Dynamitin / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / : / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BICD family-like cargo adapter 1 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 2 / Dynactin subunit 2 / Alpha-centractin / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsUrnavicius L / Lau CK
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT100387 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement.
Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter /
Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine.
History
DepositionNov 23, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f1u
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f1u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4169.png

Downloads & links

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Map

FileDownload / File: emd_4169.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the N-terminal half of two dynein tail domains bound to dynactin and BICDR1. This map was generated after particle signal subtraction from the overall map (separate deposition)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.1454998 - 0.3913671
Average (Standard dev.)-0.000013741663 (±0.0056452486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 804.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z804.000804.000804.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.1450.391-0.000

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Supplemental data

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Additional map: Map of summed signal of dynein heavy chains present in main map

Fileemd_4169_additional_1.map
AnnotationMap of summed signal of dynein heavy chains present in main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map of summed signal of dynein intermediate chains...

Fileemd_4169_additional_2.map
AnnotationMap of summed signal of dynein intermediate chains present in main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Two dynein tail domains bound to dynactin and BICDR1.

EntireName: Two dynein tail domains bound to dynactin and BICDR1.
Components
  • Complex: Two dynein tail domains bound to dynactin and BICDR1.
    • Complex: dynactin filament
      • Protein or peptide: ARP1 actin related protein 1 homolog A
      • Protein or peptide: Capping protein (Actin filament) muscle Z-line, alpha 1
      • Protein or peptide: F-actin capping protein beta subunit
      • Protein or peptide: Dynactin subunit 2
      • Protein or peptide: Dynactin subunit 2
    • Complex: Cytoplasmic dynein
      • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
      • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Complex: BICDR1
      • Protein or peptide: BICD family-like cargo adapter 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Two dynein tail domains bound to dynactin and BICDR1.

SupramoleculeName: Two dynein tail domains bound to dynactin and BICDR1. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: dynactin filament

SupramoleculeName: dynactin filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: Cytoplasmic dynein

SupramoleculeName: Cytoplasmic dynein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: BICDR1

SupramoleculeName: BICDR1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: ARP1 actin related protein 1 homolog A

MacromoleculeName: ARP1 actin related protein 1 homolog A / type: protein_or_peptide / ID: 1 / Details: ADP: adenosine diphosphate / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 42.670688 KDa
SequenceString: MESYDVIANQ PVVIDNGSGV IKAGFAGDQI PKYCFPNYVG RPKHVRVMAG ALEGDIFIGP KAEEHRGLLS IRYPMEHGIV KDWNDMERI WQYVYSKDQL QTFSEEHPVL LTEAPLNPRK NRERAAEVFF ETFNVPALFI SMQAVLSLYA TGRTTGVVLD S GDGVTHAV ...String:
MESYDVIANQ PVVIDNGSGV IKAGFAGDQI PKYCFPNYVG RPKHVRVMAG ALEGDIFIGP KAEEHRGLLS IRYPMEHGIV KDWNDMERI WQYVYSKDQL QTFSEEHPVL LTEAPLNPRK NRERAAEVFF ETFNVPALFI SMQAVLSLYA TGRTTGVVLD S GDGVTHAV PIYEGFAMPH SIMRIDIAGR DVSRFLRLYL RKEGYDFHSS SEFEIVKAIK ERACYLSINP QKDETLETEK AQ YYLPDGS TIEIGPSRFR APELLFRPDL IGEESEGIHE VLVFAIQKSD MDLRRTLFSN IVLSGGSTLF KGFGDRLLSE VKK LAPKDV KIRISAPQER LYSTWIGGSI LASLDTFKKM WVSKKEYEED GARSIHRKTF

UniProtKB: Alpha-centractin

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Macromolecule #2: Capping protein (Actin filament) muscle Z-line, alpha 1

MacromoleculeName: Capping protein (Actin filament) muscle Z-line, alpha 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 33.059848 KDa
SequenceString: MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEVDGSLKS WRESCDSALR AYVKDHYSNG FCTVYAKNID GQQTIIACIE S HQFQPKNF ...String:
MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEVDGSLKS WRESCDSALR AYVKDHYSNG FCTVYAKNID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPTAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSVTV SNEAQTAKEF IKIIEHAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGKEMQNA

UniProtKB: F-actin-capping protein subunit alpha-1

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Macromolecule #3: F-actin capping protein beta subunit

MacromoleculeName: F-actin capping protein beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 30.566627 KDa
SequenceString: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK ...String:
MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK LTSTVMLWLQ TNKSGSGTMN LGGSLTRQME KDETVSDCSP HIANIGRLVE DMENKIRSTL NEIYFGKTKD IV NGLRSVQ TFADKSKQEA LKNDLVEALK RKQQ

UniProtKB: F-actin-capping protein subunit beta

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Macromolecule #4: Dynactin subunit 2

MacromoleculeName: Dynactin subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.581965 KDa
SequenceString:
MADPKYADLP GIARNEPDVY ETSDLPEDDQ AEFDALQEEL TSTSVEHIIV

UniProtKB: Dynactin subunit 2

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Macromolecule #5: Dynactin subunit 2

MacromoleculeName: Dynactin subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 2.880144 KDa
SequenceString:
MADPKYADLP GIARNEPDVY ETSDLP

UniProtKB: Dynactin subunit 2

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Macromolecule #6: Cytoplasmic dynein 1 heavy chain 1

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.786094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES ...String:
MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES GKADRDGDKM APSVEKKIAE LEMGLLHLQQ NIEIPEISLP IHPMITNVAK QCYERGEKPK VTDFGDKVED PT FLNQLQS GVNRWIREIQ KVTKLDRDPA SGTALQEISF WLNLERALYR IQEKRESPEV LLTLDILKHG KRFHATVSFD TDT GLKQAL ETVNDYNPLM KDFPLNDLLS ATELDKIRQA LVAIFTHLRK IRNTKYPIQR ALRLVEAISR DLSSQLLKVL GTRK LMHVA YEEFEKVMVA CFEVFQTWDD EYEKLQVLLR DIVKRKREEN LKMVWRINPA HRKLQARLDQ MRKFRRQHEQ LRAVI VRVL RPQVTAVAQQ NQGEVPEPQD MKVAEVLFDA ADANAIEEVN LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRV ETR ITARLRDQLG TAKNANEMFR IFSRFNALFV RPHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRD LP PVSGSIIWAK QIDRQLTAYM KRVEDVLGKG WENHVEGQKL KQDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFTI E STRVRGRTGN VLKLKVNFLP EIITLSKEVR NLKWLGFRVP LAIVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNT ISLLVAGLKK EVQALIAEGI ALVWESYKLD PYVQRLAETV FNFQEKVDDL LIIEEKIDLE VRSLETCMYD HKTFSEILNR VQKAVDDLN LHSYSNLPIW VNKLDMEIER ILGVRLQAGL RAWTQVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV H ELRITNQV IYLNPPIEEC RYKLYQEMFA WKMVVLSLPR IQSQRYQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AV MGIVSEV EQYVKVWLQY QCLWDMQAEN IYNRLGEDLN KWQALLVQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKY DSWHKE VLSKFGQMLG SNMTEFHSQI SKSRQELEQH SVDTASTSDA VTFITYVQSL KRKIKQFEKQ

UniProtKB: Cytoplasmic dynein 1 heavy chain 1

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Macromolecule #7: Cytoplasmic dynein 1 intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 intermediate chain 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.442141 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVPPPM SPSSKSVST PSEAGSQDSG DGAVGSRRGP IKLGMAKITQ VDFPPREIVT YTKETQTPVM AQPKEDEEED DDVVAPKPPI E PEEEKTLK ...String:
MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVPPPM SPSSKSVST PSEAGSQDSG DGAVGSRRGP IKLGMAKITQ VDFPPREIVT YTKETQTPVM AQPKEDEEED DDVVAPKPPI E PEEEKTLK KDEENDSKAP PHELTEEEKQ QILHSEEFLS FFDHSTRIVE RALSEQINIF FDYSGRDLED KEGEIQAGAK LS LNRQFFD ERWSKHRVVS CLDWSSQYPE LLVASYNNNE DAPHEPDGVA LVWNMKYKKT TPEYVFHCQS AVMSATFAKF HPN LVVGGT YSGQIVLWDN RSNKRTPVQR TPLSAAAHTH PVYCVNVVGT QNAHNLISIS TDGKICSWSL DMLSHPQDSM ELVH KQSKA VAVTSMSFPV GDVNNFVVGS EEGSVYTACR HGSKAGISEM FEGHQGPITG IHCHAAVGAV DFSHLFVTSS FDWTV KLWS TKNNKPLYSF EDNAGYVYDV MWSPTHPALF ACVDGMGRLD LWNLNNDTEV PTASISVEGN PALNRVRWTH SGREIA VGD SEGQIVIYDV GEQIAVPRND EWARFGRTLA EINANRADAE EEAATRIPA

UniProtKB: Cytoplasmic dynein 1 intermediate chain 2

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Macromolecule #8: BICD family-like cargo adapter 1

MacromoleculeName: BICD family-like cargo adapter 1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.377035 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAFCLGLAG RASAPAEPDS ACCMELPAGA GDAVRSPATA AALVSFPGGP GELELALEEE LALLAAGERS SEPGEHPQAE PESPVEGHG PPLPPPPTQD PELLSVIRQK EKDLVLAARL GKALLERNQD MSRQYEQMHK ELTDKLEHLE QEKHELRRRF E NREGEWEG ...String:
MSAFCLGLAG RASAPAEPDS ACCMELPAGA GDAVRSPATA AALVSFPGGP GELELALEEE LALLAAGERS SEPGEHPQAE PESPVEGHG PPLPPPPTQD PELLSVIRQK EKDLVLAARL GKALLERNQD MSRQYEQMHK ELTDKLEHLE QEKHELRRRF E NREGEWEG RVSELETDVK QLQDELERQQ LHLREADREK TRAVQELSEQ NQRLLDQLSR ASEVERQLSM QVHALKEDFR EK NSSTNQH IIRLESLQAE IKMLSDRKRE LEHRLSATLE ENDLLQGTVE ELQDRVLILE RQGHDKDLQL HQSQLELQEV RLS YRQLQG KVEELTEERS LQSSAATSTS LLSEIEQSME AEELEQEREQ LRLQLWEAYC QVRYLCSHLR GNDSADSAVS TDSS MDESS ETSSAKDVPA GSLRTALNDL KRLIQSIVDG VEPTVTLLSV EMTALKEERD RLRVTSEDKE PKEQLQKAIR DRDEA IAKK NAVELELAKC KMDMMSLNSQ LLDAIQQKLN LSQQLEAWQD DMHRVIDRQL MDTHLKEQSR PAAAAFPRGH GVGRGQ EPS TADGKRLFSF FRKI

UniProtKB: BICD family-like cargo adapter 1

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

2860


Details: Initial model low pass filtered to 50 A
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 205611
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Details: Particle signal subtraction of areas outside this region, followed by refinement and 3D classification

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Atomic model buiding 1

RefinementSpace: REAL / Target criteria: Cross-correlation coefficient
Output model

PDB-6f1u:
N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1

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About Yorodumi

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

New format data for meta-information of EMDB entries

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