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- PDB-9ca8: Cryo-EM structure of human SRCAP-nucleosome complex in the partia... -

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Basic information

Entry
Database: PDB / ID: 9ca8
TitleCryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure)
Components
  • (DNA (285-MER)) x 2
  • Actin-related protein 6
  • Helicase SRCAP
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • RuvB-like 1
  • RuvB-like 2
  • Vacuolar protein sorting-associated protein 72 homolog
  • Zinc finger HIT domain-containing protein 1
KeywordsGENE REGULATION / Chromatin Remodeler / Snf2 family ATPase / H2A.Z
Function / homology
Function and homology information


positive regulation of lymphoid progenitor cell differentiation / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / intestinal stem cell homeostasis / regulation of DNA strand elongation / hematopoietic stem cell homeostasis / positive regulation of telomere maintenance in response to DNA damage / histone chaperone activity / establishment of protein localization to chromatin / R2TP complex ...positive regulation of lymphoid progenitor cell differentiation / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / intestinal stem cell homeostasis / regulation of DNA strand elongation / hematopoietic stem cell homeostasis / positive regulation of telomere maintenance in response to DNA damage / histone chaperone activity / establishment of protein localization to chromatin / R2TP complex / heart process / dynein axonemal particle / negative regulation of G0 to G1 transition / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / muscle cell differentiation / regulation of double-strand break repair / nucleolus organization / positive regulation of DNA damage response, signal transduction by p53 class mediator / 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 / regulation of T cell proliferation / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / somatic stem cell population maintenance / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / calcium ion homeostasis / 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 / transcription initiation-coupled chromatin remodeling / TBP-class protein binding / positive regulation of DNA repair / cellular response to estradiol stimulus / euchromatin / negative regulation of canonical Wnt signaling pathway / 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 / histone deacetylase binding / nuclear matrix / cellular response to UV / structural constituent of chromatin / UCH proteinases / transcription corepressor activity / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / nucleosome / heterochromatin formation / nucleosome assembly / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / histone binding / DNA recombination / 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 / protein heterodimerization activity / 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 / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II
Similarity search - Function
Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain ...Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal 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. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA (> 100) / Zinc finger HIT domain-containing protein 1 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 ...ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA (> 100) / Zinc finger HIT domain-containing protein 1 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Helicase SRCAP / Actin-related protein 6 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsLouder, R.K. / Park, G. / Patel, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60
Authors: Park, G. / Patel, A.B. / Wu, C. / Louder, R.K.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helicase SRCAP
B: Vacuolar protein sorting-associated protein 72 homolog
C: Actin-related protein 6
D: Zinc finger HIT domain-containing protein 1
E: RuvB-like 1
F: RuvB-like 2
G: RuvB-like 1
H: RuvB-like 2
I: RuvB-like 1
J: RuvB-like 2
Q: Histone H2A type 1
R: Histone H2B 1.1
S: Histone H2A type 1
T: Histone H2B 1.1
U: Histone H3.2
V: Histone H4
W: Histone H3.2
X: Histone H4
Y: DNA (285-MER)
Z: DNA (285-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,041,10635
Polymers1,037,24420
Non-polymers3,86215
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 10 types, 18 molecules ABCDEGIFHJQSRTUWVX

#1: Protein Helicase SRCAP / Domino homolog 2 / Snf2-related CBP activator


Mass: 343915.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562
References: UniProt: Q6ZRS2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Vacuolar protein sorting-associated protein 72 homolog / Protein YL-1 / Transcription factor-like 1


Mass: 40658.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / References: UniProt: Q15906
#3: Protein Actin-related protein 6 / hArp6 / hARPX


Mass: 45857.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / References: UniProt: Q9GZN1
#4: Protein Zinc finger HIT domain-containing protein 1 / Cyclin-G1-binding protein 1 / Zinc finger protein subfamily 4A member 1 / p18 Hamlet


Mass: 17567.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / References: UniProt: O43257
#5: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / References: UniProt: Q9Y265, DNA helicase
#6: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / References: UniProt: Q9Y230, DNA helicase
#7: Protein Histone H2A type 1


Mass: 13907.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#8: Protein Histone H2B 1.1 / H2B1.1


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#9: Protein Histone H3.2 / Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#10: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799

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DNA chain , 2 types, 2 molecules YZ

#11: DNA chain DNA (285-MER)


Mass: 87851.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain DNA (285-MER)


Mass: 88190.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 15 molecules

#13: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#14: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#15: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#16: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationN

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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
IDNameTypeDetailsEntity IDParent-IDSource
1SRCAP-nucleosome complexCOMPLEXEndogenous purified SRCAP bound to 106N32 nucleosome#1-#120NATURAL
2Endogenous human SRCAP complexCOMPLEX#1-#61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)

Cellular location: NUCLEOPLASM / Ncbi tax-ID: 9606 / Organ: BLOOD / Organelle: NUCLEUS / Organism: Homo sapiens (human) / Strain: K-562 / Tissue: BONE MARROW

IDEntity assembly-ID
21
32
Buffer solutionpH: 7.6
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 / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24701 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 100.86 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002644216
ELECTRON MICROSCOPYf_angle_d0.51360869
ELECTRON MICROSCOPYf_chiral_restr0.03946939
ELECTRON MICROSCOPYf_plane_restr0.00536837
ELECTRON MICROSCOPYf_dihedral_angle_d18.972317521

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