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- PDB-9ng0: Human SRCAP-nucleosome complex in the pre-dissociation state of t... -

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Entry
Database: PDB / ID: 9ng0
TitleHuman SRCAP-nucleosome complex in the pre-dissociation state of the H2A.Z histone exchange reaction (composite structure)
Components
  • (DNA(285-MER)) x 2
  • Actin-related protein 6
  • Helicase SRCAP
  • Histone H2A type 1
  • Histone H2A.Z
  • Histone H2B 1.1
  • Histone H2B type 1-C/E/F/G/I
  • 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 / catalytic activity, acting on a protein / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / muscle cell differentiation / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation ...positive regulation of lymphoid progenitor cell differentiation / catalytic activity, acting on a protein / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / muscle cell differentiation / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / histone chaperone activity / R2TP complex / dynein axonemal particle / Swr1 complex / establishment of protein localization to chromatin / heart process / Ino80 complex / negative regulation of transcription by RNA polymerase I / regulation of double-strand break repair / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / nucleolus organization / positive regulation of DNA damage response, signal transduction by p53 class mediator / regulation of chromosome organization / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / MLL1 complex / regulation of DNA replication / TFIID-class transcription factor complex binding / protein folding chaperone complex / Telomere Extension By Telomerase / positive regulation of transcription initiation by RNA polymerase II / cAMP/PKA signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / calcium ion homeostasis / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / regulation of embryonic development / telomere maintenance / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA helicase activity / transcription initiation-coupled chromatin remodeling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / cellular response to estradiol stimulus / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Transcriptional regulation by small RNAs / negative regulation of canonical Wnt signaling pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / chromatin DNA binding / ADP binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / beta-catenin binding / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / nuclear matrix / innate immune response in mucosa / HCMV Early Events / cellular response to UV / positive regulation of canonical Wnt signaling pathway / : / structural constituent of chromatin / transcription corepressor activity / nucleosome
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 / 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 / domain in helicases and associated with SANT domains / 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 H2A conserved site / Histone H2A signature. / Histone H2B 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. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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 H2A.Z / Histone H4 ...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 H2A.Z / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Chromatin remodeling protein SRCAP / Actin-related protein 6 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLouder, R.K. / Park, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Structural mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme.
Authors: Giho Park / Carl Wu / Robert K Louder /
Abstract: The conserved yeast SWR1 and human SRCAP chromatin remodeling complexes catalyze exchange of nucleosomal histone H2A for H2A.Z, but the underlying mechanism has remained obscure. Here, we show that ...The conserved yeast SWR1 and human SRCAP chromatin remodeling complexes catalyze exchange of nucleosomal histone H2A for H2A.Z, but the underlying mechanism has remained obscure. Here, we show that histone exchange by SRCAP requires the transient activator CFDP1 and resolve nine cryo-electron microscopy structures of the SRCAP-CFDP1 holoenzyme that define the stepwise exchange mechanism. CFDP1 recognizes the conformation of the fully engaged SRCAP-nucleosome complex through interactions with multiple subunits-including direct contact with the ATPase domain-and induces conformational transitions that drive extensive DNA unwrapping, eviction of the H2A-H2B dimer, and insertion of the H2A.Z-H2B dimer, all without necessarily requiring hydrolysis of bound ATP. Collectively, these findings provide unprecedented insight into the mechanism of activator- and nucleotide-driven histone exchange from nucleosomal H2A to H2A.Z.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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.Z
R: Histone H2B type 1-C/E/F/G/I
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)1,040,60835
Polymers1,036,74520
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 , 12 types, 18 molecules ABCDEGIFHJQRSTUWVX

#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 / Organ: BLOOD / Tissue: BONE MARROW
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 / Organ: BLOOD / Tissue: BONE MARROW / 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 / Organ: BLOOD / Tissue: BONE MARROW / 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 / Organ: BLOOD / Tissue: BONE MARROW / 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 / Organ: BLOOD / Tissue: BONE MARROW / 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 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: Q9Y230, DNA helicase
#7: Protein Histone H2A.Z / H2A/z


Mass: 13450.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AZ1, H2AFZ, H2AZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S5
#8: Protein Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone ...Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13806.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, H2BFG, HIST1H2BF, H2BC8, H2BFA, HIST1H2BG, H2BC10, H2BFK, HIST1H2BI
Production host: Escherichia coli (E. coli) / References: UniProt: P62807
#9: Protein Histone H2A type 1


Mass: 13907.163 Da / Num. of mol.: 1
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
#10: Protein Histone H2B 1.1 / H2B1.1


Mass: 13848.097 Da / Num. of mol.: 1
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
#11: 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
#12: 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

#13: DNA chain DNA(285-MER)


Mass: 87851.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: 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

#15: 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
#16: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#18: 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
IDNameTypeDetails (eV)Entity IDParent-IDSource
1SRCAP-nucleosome complexCOMPLEXEndogenous purified SRCAP bound to 106N32 nucleosome#1-#140NATURAL
2Endogenous human SRCAP complexCOMPLEX#1-#61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
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: TFS 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24877 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 91.95 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002942947
ELECTRON MICROSCOPYf_angle_d0.553458941
ELECTRON MICROSCOPYf_chiral_restr0.04266721
ELECTRON MICROSCOPYf_plane_restr0.00666773
ELECTRON MICROSCOPYf_dihedral_angle_d20.21567626

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