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- PDB-7xur: The cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE -

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Basic information

Entry
Database: PDB / ID: 7xur
TitleThe cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE
Components
  • (DNA (35-MER)) x 2
  • (snRNA-activating protein complex subunit ...) x 3
KeywordsTRANSCRIPTION/DNA / 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 / 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. / SANT domain / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...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. / SANT domain / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsWang, W. / Sun, J.F.
Funding support China, 3items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: snRNA-activating protein complex subunit 4
B: snRNA-activating protein complex subunit 3
C: snRNA-activating protein complex subunit 1
X: DNA (35-MER)
Y: DNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,8137
Polymers162,6825
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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SnRNA-activating protein complex subunit ... , 3 types, 3 molecules ABC

#1: Protein snRNA-activating protein complex subunit 4 / SNAPc subunit 4 / Proximal sequence element-binding transcription factor subunit alpha / PSE- ...SNAPc subunit 4 / Proximal sequence element-binding transcription factor subunit alpha / PSE-binding factor subunit alpha / PTF subunit alpha / snRNA-activating protein complex 190 kDa subunit / SNAPc 190 kDa subunit


Mass: 60780.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC4, SNAP190 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5SXM2
#2: Protein snRNA-activating protein complex subunit 3 / SNAPc subunit 3 / Proximal sequence element-binding transcription factor subunit beta / PSE-binding ...SNAPc subunit 3 / Proximal sequence element-binding transcription factor subunit beta / PSE-binding factor subunit beta / PTF subunit beta / Small nuclear RNA-activating complex polypeptide 3 / snRNA-activating protein complex 50 kDa subunit / SNAPc 50 kDa subunit


Mass: 46812.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC3, SNAP50 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92966
#3: Protein snRNA-activating protein complex subunit 1 / SNAPC1 / SNAPc subunit 1 / Proximal sequence element-binding transcription factor subunit gamma / PSE- ...SNAPc subunit 1 / Proximal sequence element-binding transcription factor subunit gamma / PSE-binding factor subunit gamma / PTF subunit gamma / Small nuclear RNA-activating complex polypeptide 1 / snRNA-activating protein complex 43 kDa subunit / SNAPc 43 kDa subunit


Mass: 33559.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC1, SNAP43 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16533

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DNA chain , 2 types, 2 molecules XY

#4: DNA chain DNA (35-MER)


Mass: 10726.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (35-MER)


Mass: 10803.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1the complex of human mini-SNAPc with hU6-1 PSECOMPLEX#1-#50MULTIPLE SOURCES
2human mini-SNAPcCOMPLEX#1-#31RECOMBINANT
3DNACOMPLEX#4-#51SYNTHETIC
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67058 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058030
ELECTRON MICROSCOPYf_angle_d0.66611028
ELECTRON MICROSCOPYf_dihedral_angle_d27.5091370
ELECTRON MICROSCOPYf_chiral_restr0.0421155
ELECTRON MICROSCOPYf_plane_restr0.0041250

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