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- EMDB-12799: SRP-SR at the distal site conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-12799
TitleSRP-SR at the distal site conformation
Map dataSRP-SR complex from 3D focused refinement on ribosome signal subtracted images
Sample
  • Complex: SRP-SR complex
    • Complex: SRP-SR complex
      • RNA: x 1 types
      • Protein or peptide: x 4 types
    • Complex: EM14S01-3B_G0054400.mRNA.1.CDS.1
      • Protein or peptide: x 1 types
    • Complex: Signal recognition particle receptor subunit
      • Protein or peptide: x 2 types
  • Ligand: x 3 types
KeywordsSRP SRP receptor / co-translational protein targeting / endoplasmic reticulum / signal peptide / RNA BINDING PROTEIN
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / cytoplasmic microtubule / aminopeptidase activity / vesicle-mediated transport / neutrophil chemotaxis / intracellular protein transport / GDP binding / ribosome binding / membrane => GO:0016020 / nuclear speck / serine-type endopeptidase activity / GTPase activity / endoplasmic reticulum membrane / nucleolus / GTP binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / nucleus / cytosol
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle receptor, beta subunit / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Signal recognition particle receptor beta subunit / Putative TPR-like repeat / Signal recognition particle subunit SRP68 ...Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle receptor, beta subunit / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Signal recognition particle receptor beta subunit / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / small GTPase Arf family profile. / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Longin-like domain superfamily / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Alpha/Beta hydrolase fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SRP receptor subunit alpha / EM14S01-3B_G0054400.mRNA.1.CDS.1 / Signal recognition particle receptor subunit beta / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP54 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesCanis lupus familiaris (dog) / Saccharomyces cerevisiae (brewer's yeast) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJomaa A / Ban N
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Cell Rep / Year: 2021
Title: Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.
Authors: Ahmad Jomaa / Simon Eitzinger / Zikun Zhu / Sowmya Chandrasekar / Kan Kobayashi / Shu-Ou Shan / Nenad Ban /
Abstract: Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many ...Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles. Due to its complexity, the mammalian SRP targeting process is mechanistically not well understood. In particular, it is not clear how SRP recognizes translating ribosomes with exposed signal sequences and how the GTPase activity of SRP and SR is regulated. Here, we present electron cryo-microscopy structures of SRP and SRP·SR in complex with the translating ribosome. The structures reveal the specific molecular interactions between SRP and the emerging signal sequence and the elements that regulate GTPase activity of SRP·SR. Our results suggest the molecular mechanism of how eukaryote-specific elements regulate the early and late stages of SRP-dependent protein targeting.
#1: Journal: Cell Rep / Year: 2021
Title: Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle
Authors: Jomaa A / Eitzinger S / Zhu Z / Chandrasekar S / Kobayashi K / Shan S / Ban N
History
DepositionApr 23, 2021-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by radius
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  • Surface view with fitted model
  • Atomic models: PDB-7obq
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7obq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12799.png

Downloads & links

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Map

FileDownload / File: emd_12799.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSRP-SR complex from 3D focused refinement on ribosome signal subtracted images
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.024083594 - 0.049472265
Average (Standard dev.)0.0003989505 (±0.0018282081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 479.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z479.360479.360479.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0240.0490.000

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Supplemental data

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Sample components

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Entire : SRP-SR complex

EntireName: SRP-SR complex
Components
  • Complex: SRP-SR complex
    • Complex: SRP-SR complex
      • RNA: SRP RNA
      • Protein or peptide: Signal recognition particle 19
      • Protein or peptide: Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68
      • Protein or peptide: Signal recognition particle 54 kDa protein
      • Protein or peptide: Signal recognition particle subunit SRP72
    • Complex: EM14S01-3B_G0054400.mRNA.1.CDS.1
      • Protein or peptide: EM14S01-3B_G0054400.mRNA.1.CDS.1
    • Complex: Signal recognition particle receptor subunit
      • Protein or peptide: Signal recognition particle receptor subunit beta
      • Protein or peptide: SRP receptor subunit alpha
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

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Supramolecule #1: SRP-SR complex

SupramoleculeName: SRP-SR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: SRP-SR complex

SupramoleculeName: SRP-SR complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4, #6, #8
Source (natural)Organism: Canis lupus familiaris (dog)

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Supramolecule #3: EM14S01-3B_G0054400.mRNA.1.CDS.1

SupramoleculeName: EM14S01-3B_G0054400.mRNA.1.CDS.1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #4: Signal recognition particle receptor subunit

SupramoleculeName: Signal recognition particle receptor subunit / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5, #7
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: SRP RNA

MacromoleculeName: SRP RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 80.701867 KDa
SequenceString: GCCGGGCGCG GUGGCGCGCG CCUGUAGUCC CAGCUACUCG GGAGGCUGAG GCAGGAGGAU CGCUUCGCUA UGCCGAUCGG GUGUCCGCA CUAAGUUCGG CAUCAAUAUG GUGACCUCCC GGGAGCGGGG GACCACCAGG UUGCCUAAGG AGGGGUGAAC C GGCCCAGG ...String:
GCCGGGCGCG GUGGCGCGCG CCUGUAGUCC CAGCUACUCG GGAGGCUGAG GCAGGAGGAU CGCUUCGCUA UGCCGAUCGG GUGUCCGCA CUAAGUUCGG CAUCAAUAUG GUGACCUCCC GGGAGCGGGG GACCACCAGG UUGCCUAAGG AGGGGUGAAC C GGCCCAGG UCGGAAACGG AGCAGGUCAA AACUCCCGUG CUGAUCAGUA GUGGGAUCGC GCCUGUGAAU AGCAUAGCGA GA CCCCGUC UC

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Macromolecule #2: Signal recognition particle 19

MacromoleculeName: Signal recognition particle 19 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 16.183746 KDa
SequenceString:
MACAAARSPA EQDRFICIYP AYLNNKKTIA EGRRIPISKA VENPTATEIQ DVCSAVGLNV FLEKNKMYSR EWNRDVQYRG RVRVQLKQE DGSLCLVQFP SRKSVMLYAA EMIPKLKTRT QKTGGGDQSL QQGEGSKKGK GKKKK

UniProtKB: Signal recognition particle 19 kDa protein

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Macromolecule #3: EM14S01-3B_G0054400.mRNA.1.CDS.1

MacromoleculeName: EM14S01-3B_G0054400.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.294518 KDa
Recombinant expressionOrganism: Oryctolagus cuniculus (rabbit)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: EM14S01-3B_G0054400.mRNA.1.CDS.1

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Macromolecule #4: Signal recognition particle subunit SRP68,Signal recognition part...

MacromoleculeName: Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 67.082898 KDa
SequenceString: MAAEKQVPGG GGGGGGGGGG GGGSGGGRGA GGEENKENER PSAGSKANRE FGDSLSLEIL QIIKESQQQH GLRHGDFQRY RGYCSRRQR RLRKTLNFKM GNRHKFTGKK VTEDLLTDNR YLLLVLMDAE RAWSYAMQLK QEANTEPRKR FHLLSRLRKA V KHAEELER ...String:
MAAEKQVPGG GGGGGGGGGG GGGSGGGRGA GGEENKENER PSAGSKANRE FGDSLSLEIL QIIKESQQQH GLRHGDFQRY RGYCSRRQR RLRKTLNFKM GNRHKFTGKK VTEDLLTDNR YLLLVLMDAE RAWSYAMQLK QEANTEPRKR FHLLSRLRKA V KHAEELER LCESNRVDAK TKLEAQAYTA YLSGMLRFEH QEWKAAIEAF NKCKTIYEKL ASAFTEEQAV LYNQRVEEIS PN IRYCAYN IGDQSAINEL MQMRLRSGGT EGLLAEKLEA LITQTRAKQA ATMSEVEWRG RTVPVKIDKV RIFLLGLADN EAA IAQAES EETKERLFES MLSECRDAIQ AVREELKPDQ KQRDYTLDGE SGKVSNLQYL HSYLTYIKLS TAIRRNENMA KGLQ KALQQ QPEDESKRSP RPQDLIRLYD IILQNLVELL QLPGLEEDRA FQKEIGLKTL VFKAYRCFFI AQSYVLVKKW SEALV LYDR VLKYANEVN(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)

UniProtKB: Signal recognition particle subunit SRP68, Signal recognition particle subunit SRP68

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Macromolecule #5: Signal recognition particle receptor subunit beta

MacromoleculeName: Signal recognition particle receptor subunit beta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 29.846182 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASADSRRLG DGDGAGGAFQ PYLDSLRQEL QQRDPTVLSV VVALLAVLLT LVFWKLVRSR RSSQRAVLLL GLCDSGKTLL FVRLLTGHY RDTQTSITDS SATYRVNNNR GNSLTLIDLP GHESLRLQFL ERFKTSARAV VFVVDSAAFQ REVKDVAEFL Y QVLIDSMS ...String:
MASADSRRLG DGDGAGGAFQ PYLDSLRQEL QQRDPTVLSV VVALLAVLLT LVFWKLVRSR RSSQRAVLLL GLCDSGKTLL FVRLLTGHY RDTQTSITDS SATYRVNNNR GNSLTLIDLP GHESLRLQFL ERFKTSARAV VFVVDSAAFQ REVKDVAEFL Y QVLIDSMS LKNTPSFLIA CNKQDIAMAK SAKLIQQQLE KELNTLRVTR SAAPSTLDSS STAPAQLGKK GKEFEFSQLP LK VEFLECS AKGGRGDPGS ADIQDLEKWL AKIA

UniProtKB: Signal recognition particle receptor subunit beta

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Macromolecule #6: Signal recognition particle 54 kDa protein

MacromoleculeName: Signal recognition particle 54 kDa protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 55.775672 KDa
SequenceString: MVLADLGRKI TSALRSLSNA TIINEEVLNA MLKEVCTALL EADVNIKLVK QLRENVKSAI DLEEMASGLN KRKMIQHAVF KELVKLVDP GVKAWTPTKG KQNVIMFVGL QGSGKTTTCS KLAYYYQRKG WKTCLICADT FRAGAFDQLK QNATKARIPF Y GSYTEMDP ...String:
MVLADLGRKI TSALRSLSNA TIINEEVLNA MLKEVCTALL EADVNIKLVK QLRENVKSAI DLEEMASGLN KRKMIQHAVF KELVKLVDP GVKAWTPTKG KQNVIMFVGL QGSGKTTTCS KLAYYYQRKG WKTCLICADT FRAGAFDQLK QNATKARIPF Y GSYTEMDP VIIASEGVEK FKNENFEIII VDTSGRHKQE DSLFEEMLQV ANAIQPDNIV YVMDASIGQA CEAQAKAFKD KV DVASVIV TKLDGHAKGG GALSAVAATK SPIIFIGTGE HIDDFEPFKT QPFISKLLGM GDIEGLIDKV NELKLDDNEA LIE KLKHGQ FTLRDMYEQF QNIMKMGPFS QILGMIPGFG TDFMSKGNEQ ESMARLKKLM TIMDSMNDQE LDSTDGAKVF SKQP GRIQR VARGSGVSTR DVQELLTQYT KFAQMVKKMG GIKGLFKGGD MSKNVSQSQM AKLNQQMAKM MDPRVLHHMG GMAGL QSMM RQFQQGAAGN MKGMMGFNNM

UniProtKB: Signal recognition particle subunit SRP54

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Macromolecule #7: SRP receptor subunit alpha

MacromoleculeName: SRP receptor subunit alpha / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 69.745945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLDFFTIFSK GGLVLWCFQG VSDSCTGPVN ALIRSVLLQE RGGNNSFTHE ALTLKYKLDN QFELVFVVGF QKILTLTYVD KLIDDVHRL FRDKYRTEIQ QQSALSLLNG TFDFQNDFLR LLREAEESSK IRAPTTMKKF EDSEKAKKPV RSMIETRGEK P KEKAKNSK ...String:
MLDFFTIFSK GGLVLWCFQG VSDSCTGPVN ALIRSVLLQE RGGNNSFTHE ALTLKYKLDN QFELVFVVGF QKILTLTYVD KLIDDVHRL FRDKYRTEIQ QQSALSLLNG TFDFQNDFLR LLREAEESSK IRAPTTMKKF EDSEKAKKPV RSMIETRGEK P KEKAKNSK KKGAKKEGSD GPLATSKAVP AEKSGLPVGP ENGVELSKEE LIRRKREEFI QKHGRGLEKS SKSKSEAPKE KG KKAPRVW ELGGCANKEV LDYSTPTTNG APEAALSEDI NLIRGTGPGG QLQDLDCSSS DDEGAAQNST KPSSTKGTLG GMF GMLKGL VGSKSLSRED MESVLDKMRD HLIAKNVAAD IAVQLCESVA NKLEGKVMGT FSTVTSTVKQ ALQESLVQIL QPQR RVDML RDIMDAQRRQ RPYVVTFCGV NGVGKSTNLA KISFWLLENG FSVLIAACDT FRAGAVEQLR THTRRLSALH PPEKH GGRT MVQLFEKGYG KDAAGIAMEA IAFARNQGFD VVLVDTAGRM QDNAPLMTAL AKLITVNTPD LVLFVGEALV GNEAVD QLV KFNRALADHS MAQTPRLIDG IVLTKFDTID DKVGAAISMT YITSKPIVFV GTGQTYCDLR SLNAKAVVAA LMKA

UniProtKB: SRP receptor subunit alpha

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Macromolecule #8: Signal recognition particle subunit SRP72

MacromoleculeName: Signal recognition particle subunit SRP72 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 74.608102 KDa
SequenceString: MASGGSGGVS VPALWSEVNR YGQNGDFTRA LKTVNKILQI NKDDVTALHC KVVCLIQNGS FKEALNVINT HTKVLANNSL SFEKAYCEY RLNRIENALK TIESANQQTD KLKELYGQVL YRLERYDECL AVYRDLVRNS QDDYDEERKT NLSAVVAAQS N WEKVVPEN ...String:
MASGGSGGVS VPALWSEVNR YGQNGDFTRA LKTVNKILQI NKDDVTALHC KVVCLIQNGS FKEALNVINT HTKVLANNSL SFEKAYCEY RLNRIENALK TIESANQQTD KLKELYGQVL YRLERYDECL AVYRDLVRNS QDDYDEERKT NLSAVVAAQS N WEKVVPEN LGLQEGTHEL CYNAACALIG QGQLSQAMKI LQKAEDLCRR SLSEDSDGTE EDPQAELAII HGQMAYILQL QG RTEEALQ LYNQIIKLKP TDVGLLAVIA NNIITINKDQ NVFDSKKKVK LTNAEGVEFK LSKKQLQAIE FNKALLAMYT NQA EQCRKI SASLQSQSPE HLLPVLIQAA QLCREKQHTK AIELLQEFSD QHPENAAEIK LTMAQLKISQ GNISKACLIL RSIE ELKHK PGMVSALVTM YSHEEDIDSA IEVFTQAIQW YQNHQPKSSA HLSLIREAAN FKLKYGRKKE AISDLEQLWK QNPKD IHTL AQLISAYSLV DPEKAKALSK HLPSSDSMSL KVDVEALENS PGATYIRKKG GKVAGDSQPK EQGQGDLKKK KKKKKG KLP KNYDPKVTPD PERWLPMRER SYYRGRKKGK KKDQIGKGTQ GATAGASSEL DASKTVSSPP TSPRPGSAAT ASASTSN II PPRHQKPAGA PATKKKQQQK KKKGGKGGW

UniProtKB: Signal recognition particle subunit SRP72

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 11 / Number of copies: 2 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*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: 7.5
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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

Startup modelType of model: OTHER / Details: From initial reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 155989
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6frk


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7obq:
SRP-SR at the distal site conformation

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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