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Yorodumi- EMDB-33477: the cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33477 | ||||||||||||
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Title | the cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | snRNA / Transcription factor / Complex / PSE. / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||||||||
Function / homology | Function and homology information snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II general transcription initiation factor activity ...snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II general transcription initiation factor activity / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / nucleolus / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||||||||
Authors | Wang W / Sun JF | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Authors: Jianfeng Sun / Xue Li / Xuben Hou / Sujian Cao / Wenjin Cao / Ye Zhang / Jinyang Song / Manfu Wang / Hao Wang / Xiaodong Yan / Zengpeng Li / Robert G Roeder / Wei Wang / Abstract: In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA ...In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a "wrap-around" mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33477.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-33477-v30.xml emd-33477.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
Images | emd_33477.png | 52.8 KB | ||
Filedesc metadata | emd-33477.cif.gz | 6.4 KB | ||
Others | emd_33477_half_map_1.map.gz emd_33477_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33477 | HTTPS FTP |
-Validation report
Summary document | emd_33477_validation.pdf.gz | 793.8 KB | Display | EMDB validaton report |
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Full document | emd_33477_full_validation.pdf.gz | 793.4 KB | Display | |
Data in XML | emd_33477_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_33477_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33477 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33477 | HTTPS FTP |
-Related structure data
Related structure data | 7xurMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33477.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33477_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33477_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the complex of human mini-SNAPc with hU6-1 PSE
Entire | Name: the complex of human mini-SNAPc with hU6-1 PSE |
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Components |
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-Supramolecule #1: the complex of human mini-SNAPc with hU6-1 PSE
Supramolecule | Name: the complex of human mini-SNAPc with hU6-1 PSE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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-Supramolecule #2: human mini-SNAPc
Supramolecule | Name: human mini-SNAPc / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5 |
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-Macromolecule #1: snRNA-activating protein complex subunit 4
Macromolecule | Name: snRNA-activating protein complex subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60.780254 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DYKDDDDKSL EVLFQGPMDV DAEREKITQE IKELERILDP GSSGSHVEIS ESSLESDSEA DSLPSEDLDP ADPPISEEER WGEASNDED DPKDKTLPED PETCLQLNMV YQEVIQEKLA EANLLLAQNR EQQEELMRDL AGSKGTKVKD GKSLPPSTYM G HFMKPYFK ...String: DYKDDDDKSL EVLFQGPMDV DAEREKITQE IKELERILDP GSSGSHVEIS ESSLESDSEA DSLPSEDLDP ADPPISEEER WGEASNDED DPKDKTLPED PETCLQLNMV YQEVIQEKLA EANLLLAQNR EQQEELMRDL AGSKGTKVKD GKSLPPSTYM G HFMKPYFK DKVTGVGPPA NEDTREKAAQ GIKAFEELLV TKWKNWEKAL LRKSVVSDRL QRLLQPKLLK LEYLHQKQSK VS SELERQA LEKQGREAEK EIQDINQLPE EALLGNRLDS HDWEKISNIN FEGSRSAEEI RKFWQNSEHP SINKQEWSRE EEE RLQAIA AAHGHLEWQK IAEELGTSRS AFQCLQKFQQ HNKALKRKEW TEEEDRMLTQ LVQEMRVGSH IPYRRIVYYM EGRD SMQLI YRWTKSLDPG LKKGYWAPEE DAKLLQAVAK YGEQDWFKIR EEVPGRSDAQ CRDRYLRRLH FSLKKGRWNL KEEEQ LIEL IEKYGVGHWA KIASELPHRS GSQCLSKWKI MMGKKQGL UniProtKB: snRNA-activating protein complex subunit 4 |
-Macromolecule #2: snRNA-activating protein complex subunit 3
Macromolecule | Name: snRNA-activating protein complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.812605 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAEGSRGGPT CSGVGGRQDP VSGSGGCNFP EYELPELNTR AFHVGAFGEL WRGRLRGAGD LSLREPPASA LPGSQAADSD REDAAVARD LDCSLEAAAE LRAVCGLDKL KCLEDGEDPE VIPENTDLVT LGVRKRFLEH REETITIDRA CRQETFVYEM E SHAIGKKP ...String: MAEGSRGGPT CSGVGGRQDP VSGSGGCNFP EYELPELNTR AFHVGAFGEL WRGRLRGAGD LSLREPPASA LPGSQAADSD REDAAVARD LDCSLEAAAE LRAVCGLDKL KCLEDGEDPE VIPENTDLVT LGVRKRFLEH REETITIDRA CRQETFVYEM E SHAIGKKP ENSADMIEEG ELILSVNILY PVIFHKHKEH KPYQTMLVLG SQKLTQLRDS IRCVSDLQIG GEFSNTPDQA PE HISKDLY KSAFFYFEGT FYNDKRYPEC RDLSRTIIEW SESHDRGYGK FQTARMEDFT FNDLCIKLGF PYLYCHQGDC EHV IVITDI RLVHHDDCLD RTLYPLLIKK HWLWTRKCFV CKMYTARWVT NNDSFAPEDP CFFCDVCFRM LHYDSEGNKL GEFL AYPYV DPGTFN UniProtKB: snRNA-activating protein complex subunit 3 |
-Macromolecule #3: snRNA-activating protein complex subunit 1
Macromolecule | Name: snRNA-activating protein complex subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 33.559516 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HHHHHHSENL YFQGMGTPPG LQTDCEALLS RFQETDSVRF EDFTELWRNM KFGTIFCGRM RNLEKNMFTK EALALAWRYF LPPYTFQIR VGALYLLYGL YNTQLCQPKQ KIRVALKDWD EVLKFQQDLV NAQHFDAAYI FRKLRLDRAF HFTAMPKLLS Y RMKKKIHR ...String: HHHHHHSENL YFQGMGTPPG LQTDCEALLS RFQETDSVRF EDFTELWRNM KFGTIFCGRM RNLEKNMFTK EALALAWRYF LPPYTFQIR VGALYLLYGL YNTQLCQPKQ KIRVALKDWD EVLKFQQDLV NAQHFDAAYI FRKLRLDRAF HFTAMPKLLS Y RMKKKIHR AEVTEEFKDP SDRVMKLITS DVLEEMLNVH DHYQNMKHVI SVDKSKPDKA LSLIKDDFFD NIKNIVLEHQ QW HKDRKNP SLKSKTNDGE EKMEGNSQET ERCERAESLA KIKSK UniProtKB: snRNA-activating protein complex subunit 1 |
-Macromolecule #4: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.72693 KDa |
Sequence | String: (DT)(DC)(DA)(DT)(DA)(DT)(DG)(DC)(DT)(DT) (DA)(DC)(DC)(DG)(DT)(DA)(DA)(DC)(DT)(DT) (DG)(DA)(DA)(DA)(DG)(DT)(DA)(DT)(DT) (DT)(DC)(DG)(DA)(DT)(DT) |
-Macromolecule #5: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.803009 KDa |
Sequence | String: (DA)(DA)(DT)(DC)(DG)(DA)(DA)(DA)(DT)(DA) (DC)(DT)(DT)(DT)(DC)(DA)(DA)(DG)(DT)(DT) (DA)(DC)(DG)(DG)(DT)(DA)(DA)(DG)(DC) (DA)(DT)(DA)(DT)(DG)(DA) |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67058 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Details: cryosparc stochastic gradient descent |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |