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- PDB-6igm: Cryo-EM Structure of Human SRCAP Complex -

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Basic information

Entry
Database: PDB / ID: 6igm
TitleCryo-EM Structure of Human SRCAP Complex
Components
  • Actin-related protein 6
  • Helicase SRCAP
  • RuvB-like 1
  • RuvB-like 2
  • unknown subunit
KeywordsTRANSCRIPTION / SRCAP complex
Function / homology
Function and homology information


promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex ...promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / regulation of double-strand break repair / nucleolus organization / box C/D snoRNP assembly / protein folding chaperone complex / negative regulation of transcription by RNA polymerase I / regulation of chromosome organization / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / TFIID-class transcription factor complex binding / regulation of DNA replication / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / telomere maintenance / DNA helicase activity / TBP-class protein binding / positive regulation of DNA repair / cellular response to estradiol stimulus / negative regulation of canonical Wnt signaling pathway / euchromatin / Formation of the beta-catenin:TCF transactivating complex / helicase activity / DNA Damage Recognition in GG-NER / ADP binding / beta-catenin binding / chromatin DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / cellular response to UV / UCH proteinases / transcription corepressor activity / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / nucleosome / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / histone binding / DNA helicase / transcription coactivator activity / cytoskeleton / regulation of cell cycle / Ub-specific processing proteases / protein stabilization / nuclear speck / nuclear body / ciliary basal body / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / ribonucleoprotein complex / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
RuvBL1 DNA/RNA binding domain / : / domain in helicases and associated with SANT domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain ...RuvBL1 DNA/RNA binding domain / : / domain in helicases and associated with SANT domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Helicase, Ruva Protein; domain 3 - #60 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase, Ruva Protein; domain 3 / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Helicase SRCAP / Actin-related protein 6 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsFeng, Y. / Tian, Y. / Wu, Z. / Xu, Y.
CitationJournal: Cell Res / Year: 2018
Title: Cryo-EM structure of human SRCAP complex.
Authors: Yangyang Feng / Yuan Tian / Zihan Wu / Yanhui Xu /
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: RuvB-like 1
B: RuvB-like 2
C: RuvB-like 1
D: RuvB-like 2
E: RuvB-like 1
F: RuvB-like 2
G: Actin-related protein 6
H: Helicase SRCAP
X: unknown subunit


Theoretical massNumber of molelcules
Total (without water)699,6269
Polymers699,6269
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RuvB-like 1 / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa ...49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 50296.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A
Production host: mammal environmental sample (environmental samples)
References: UniProt: Q9Y265, DNA helicase
#2: Protein RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 51222.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46
Production host: mammal environmental sample (environmental samples)
References: UniProt: Q9Y230, DNA helicase
#3: Protein Actin-related protein 6 / hArp6 / hARPX


Mass: 45857.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR6, CDA12
Production host: mammal environmental sample (environmental samples)
References: UniProt: Q9GZN1
#4: Protein Helicase SRCAP / Domino homolog 2 / Snf2-related CBP activator


Mass: 343915.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRCAP, KIAA0309
Production host: mammal environmental sample (environmental samples)
References: UniProt: Q6ZRS2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#5: Protein unknown subunit


Mass: 5294.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: mammal environmental sample (environmental samples)

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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

ComponentName: SRCAP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: mammal environmental sample (environmental samples)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.5625 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130318 / Symmetry type: POINT

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