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- EMDB-33477: the cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE -

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Basic information

Entry
Database: EMDB / ID: EMD-33477
Titlethe cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE
Map data
Sample
  • Complex: the complex of human mini-SNAPc with hU6-1 PSE
    • Complex: human mini-SNAPc
      • Protein or peptide: snRNA-activating protein complex subunit 4
      • Protein or peptide: snRNA-activating protein complex subunit 3
      • Protein or peptide: snRNA-activating protein complex subunit 1
    • Complex: DNA
      • DNA: DNA (35-MER)
      • DNA: DNA (35-MER)
  • Ligand: ZINC ION
KeywordssnRNA / 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 / RNA polymerase II transcribes snRNA genes / transcription by RNA polymerase III / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / nucleolus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / : / Myb-like domain profile. / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / SANT domain ...snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / : / Myb-like domain profile. / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
snRNA-activating protein complex subunit 1 / snRNA-activating protein complex subunit 4 / snRNA-activating protein complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsWang W / Sun JF
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171207 China
National Natural Science Foundation of China (NSFC)31970584 China
National Natural Science Foundation of China (NSFC)32000857 China
CitationJournal: 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
DepositionMay 19, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33477.png

Downloads & links

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Map

FileDownload / File: emd_33477.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 322.8 Å		1.08 Å/pix.
x 300 pix.
= 322.8 Å		1.08 Å/pix.
x 300 pix.
= 322.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.2394304 - 3.6847749
Average (Standard dev.)-0.00045605298 (±0.047970727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 322.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33477_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33477_half_map_2.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 : the complex of human mini-SNAPc with hU6-1 PSE

EntireName: the complex of human mini-SNAPc with hU6-1 PSE
Components
  • Complex: the complex of human mini-SNAPc with hU6-1 PSE
    • Complex: human mini-SNAPc
      • Protein or peptide: snRNA-activating protein complex subunit 4
      • Protein or peptide: snRNA-activating protein complex subunit 3
      • Protein or peptide: snRNA-activating protein complex subunit 1
    • Complex: DNA
      • DNA: DNA (35-MER)
      • DNA: DNA (35-MER)
  • Ligand: ZINC ION

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Supramolecule #1: the complex of human mini-SNAPc with hU6-1 PSE

SupramoleculeName: 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

SupramoleculeName: human mini-SNAPc / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5

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Macromolecule #1: snRNA-activating protein complex subunit 4

MacromoleculeName: snRNA-activating protein complex subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.780254 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: snRNA-activating protein complex subunit 3

MacromoleculeName: snRNA-activating protein complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.812605 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #3: snRNA-activating protein complex subunit 1

MacromoleculeName: snRNA-activating protein complex subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.559516 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #4: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.72693 KDa
SequenceString:
(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)

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Macromolecule #5: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.803009 KDa
SequenceString:
(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)

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67058
Initial angle assignmentType: RANDOM ASSIGNMENT / Details: cryosparc stochastic gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD

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