EMDB-4960: PFV intasome - nucleosome strand transfer complex

Basic information

• Entry: Database: EMDB / ID: EMD-4960
• Title: PFV intasome - nucleosome strand transfer complex
• Map data: Nucleosome core particle bound by PFV intasome post catalytic state

Sample

• Complex: Nucleosome core particle bound by PFV intasome post in the post catalytic state
  • Complex: Nucleosome
    • Protein or peptide: x 4 types
  • Complex: Integrase
    • Protein or peptide: x 1 types
  • Complex: Human DNA
    • DNA: x 4 types
  • Complex: DNA
    • DNA: x 1 types
• Ligand: x 1 types

• Keywords: chromatin / nucleosome / retrovirus / DNA BINDING PROTEIN

Function / homology

Function:

negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / nucleus organization / spermatid development / subtelomeric heterochromatin formation / single fertilization / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / virion component / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / DNA integration / viral genome integration into host DNA / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA-directed DNA polymerase / establishment of integrated proviral latency / HCMV Early Events / viral penetration into host nucleus / Transcriptional regulation of granulopoiesis / osteoblast differentiation / male gonad development / structural constituent of chromatin / RNA-directed DNA polymerase activity / UCH proteinases / RNA-DNA hybrid ribonuclease activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleosome / host cell / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / host cell cytoplasm / cell population proliferation / DNA-directed DNA polymerase / chromosome, telomeric region

Domain/homology:

Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Histone-fold / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily

Component:

Histone H2A type 1 / Pro-Pol polyprotein / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.3

• Biological species: Homo sapiens (human) / Human spumaretrovirus / Pyrobaculum filamentous virus 1
• Method: single particle reconstruction / cryo EM / Resolution: 3.9 Å
• Authors: Renault L / Maskell DP / Wilson MD / Cherepanov P / Costa A

Funding support

United Kingdom, 2 items

Organization	Grant number	Country
The Francis Crick Institute	FC0010061	United Kingdom
The Francis Crick Institute	FC0010065	United Kingdom

• Citation: Journal: Nat Commun / Year: 2019; Title: Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.; Authors: Marcus D Wilson / Ludovic Renault / Daniel P Maskell / Mohamed Ghoneim / Valerie E Pye / Andrea Nans / David S Rueda / Peter Cherepanov / Alessandro Costa / ; Abstract: Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers.

History

Deposition	May 9, 2019	-
Header (metadata) release	Sep 25, 2019	-
Map release	Sep 25, 2019	-
Update	May 22, 2024	-
Current status	May 22, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_4960.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Nucleosome core particle bound by PFV intasome post catalytic state
• Voxel size: X=Y=Z: 1.111 Å

Density

Contour Level	By AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum	-0.33225438 - 0.65916705
Average (Standard dev.)	0.0013075157 (±0.014830548)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 240 240 240 Spacing 240 240 240
Cell	A=B=C: 266.63998 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.111	1.111	1.111
M x/y/z	240	240	240
origin x/y/z	0.000	0.000	0.000
length x/y/z	266.640	266.640	266.640
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	858	858	858
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	240	240	240
D min/max/mean	-0.332	0.659	0.001

Supplemental data

Half map: Half map 1 of Nucleosome core particle bound...

• File: emd_4960_half_map_1.map
• Annotation: Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state

Half map: Half map 1 of Nucleosome core particle bound...

• File: emd_4960_half_map_2.map
• Annotation: Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state

Sample components

Entire : Nucleosome core particle bound by PFV intasome post in the post c...

• Entire: Name: Nucleosome core particle bound by PFV intasome post in the post catalytic state

Components

• Complex: Nucleosome core particle bound by PFV intasome post in the post catalytic state
  • Complex: Nucleosome
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
  • Complex: Integrase
    • Protein or peptide: Integrase
  • Complex: Human DNA
    • DNA: DNA (128-MER)
    • DNA: DNA (108-MER)
    • DNA: DNA (33-MER)
    • DNA: DNA (53-MER)
  • Complex: DNA
    • DNA: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')
• Ligand: MAGNESIUM ION

Supramolecule #1: Nucleosome core particle bound by PFV intasome post in the post c...

• Supramolecule: Name: Nucleosome core particle bound by PFV intasome post in the post catalytic state; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10; Details: human histones refolded as an octamer with native human D02 sequence. PFV intasome formed form short annealed oligos and PFV integrase. complex formed by mixing and separated by SEC. Catalysis initiated by addition of Magnesium ions
• Molecular weight: Theoretical: 399 KDa

Supramolecule #2: Nucleosome

• Supramolecule: Name: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: Nucleosome
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #3: Integrase

• Supramolecule: Name: Integrase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5 / Details: Integrase
• Source (natural): Organism: Human spumaretrovirus

Supramolecule #4: Human DNA

• Supramolecule: Name: Human DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#9 / Details: Human DNA
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #5: DNA

• Supramolecule: Name: DNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #10 / Details: DNA
• Source (natural): Organism: Pyrobaculum filamentous virus 1

Macromolecule #1: Histone H3.3

• Macromolecule: Name: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.360983 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

Macromolecule #2: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.394426 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

Macromolecule #3: Histone H2A type 1

• Macromolecule: Name: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.121537 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1

Macromolecule #4: Histone H2B type 1-C/E/F/G/I

• Macromolecule: Name: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.937213 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

Macromolecule #5: Integrase

• Macromolecule: Name: Integrase / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
• Source (natural): Organism: Human spumaretrovirus
• Molecular weight: Theoretical: 44.456695 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GPGCNTKKPN LDAELDQLLQ GHYIKGYPKQ YTYFLEDGKV KVSRPEGVKI IPPQSDRQKI VLQAHNLAHT GREATLLKIA NLYWWPNMR KDVVKQLGRC QQCLITNASN KASGPILRPD RPQKPFDKFF IDYIGPLPPS QGYLYVLVVV DGMTGFTWLY P TKAPSTSA TVKSLNVLTS IAIPKVIHSD QGAAFTSSTF AEWAKERGIH LEFSTPYHPQ SSGKVERKNS DIKRLLTKLL VG RPTKWYD LLPVVQLALN NTYSPVLKYT PHQLLFGIDS NTPFANQDTL DLTREEELSL LQEIRTSLYH PSTPPASSRS WSP VVGQLV QERVARPASL RPRWHKPSTV LKVLNPRTVV ILDHLGNNRT VSIDNLKPTS HQNGTTNDTA TMDHLEKNE

UniProtKB: Pro-Pol polyprotein

Macromolecule #6: DNA (128-MER)

• Macromolecule: Name: DNA (128-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 39.189094 KDa

Sequence

String:

(DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DA)(DC)(DA)(DC)(DT)(DA)(DC) (DC)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DG) (DA)(DA)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT) (DC) (DA)(DC)(DC)(DA)(DG)(DC)(DC)(DA) (DG)(DG)(DC)(DC)(DT)(DT)(DG)(DA)(DA)(DT) (DG)(DC) (DA)(DA)(DT)(DT)(DG)(DT)(DC) (DT)(DT)(DA)(DC)(DT)(DA)(DG)(DG)(DA)(DA) (DT)(DA)(DT) (DT)(DT)(DG)(DG)(DA)(DC) (DT)(DT)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DT) (DA)(DC)(DC)(DA) (DT)(DT)(DC)(DA)(DG) (DG)(DT)(DA)(DA)(DC)(DT)(DT)(DG)(DA)(DT) (DA)(DC)(DA)(DA)(DA) (DC)(DA)(DC)(DA) (DG)(DC)(DC)(DC)

Macromolecule #7: DNA (108-MER)

• Macromolecule: Name: DNA (108-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 33.581453 KDa

Sequence

String:

(DG)(DG)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT) (DT)(DG)(DT)(DA)(DT)(DC)(DA)(DA)(DG)(DT) (DT)(DA)(DC)(DC)(DT)(DG)(DA)(DA)(DT) (DG)(DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG) (DG) (DA)(DA)(DG)(DT)(DC)(DC)(DA)(DA) (DA)(DT)(DA)(DT)(DT)(DC)(DC)(DT)(DA)(DG) (DT)(DA) (DA)(DG)(DA)(DC)(DA)(DA)(DT) (DT)(DG)(DC)(DA)(DT)(DT)(DC)(DA)(DA)(DG) (DG)(DC)(DC) (DT)(DG)(DG)(DC)(DT)(DG) (DG)(DT)(DG)(DA)(DA)(DA)(DC)(DC)(DT)(DG) (DT)(DT)(DT)(DC) (DC)(DT)(DG)(DG)(DG) (DA)(DA)(DG)

Macromolecule #8: DNA (33-MER)

• Macromolecule: Name: DNA (33-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 10.114523 KDa

Sequence

String:

(DG)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DT)(DC) (DT)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG)(DT) (DG)(DA)(DA)(DA)(DA)(DC)(DC)(DA)(DA) (DC)(DT)(DA)(DA)

Macromolecule #9: DNA (53-MER)

• Macromolecule: Name: DNA (53-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 16.397531 KDa

Sequence

String:

(DG)(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DA)(DC)(DA)(DG)(DT)(DA)(DG) (DT)(DT)(DA)(DG)(DT)(DT)(DG)(DG)(DT) (DT)(DT)(DT)(DC)(DA)(DC)(DC)(DA)(DC)(DA) (DG) (DG)(DG)(DA)(DG)(DA)(DA)(DC)(DC) (DT)(DG)(DG)(DA)(DC)

Macromolecule #10: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')

• Macromolecule: Name: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3'); type: dna / ID: 10 / Number of copies: 2 / Classification: DNA
• Source (natural): Organism: Pyrobaculum filamentous virus 1
• Molecular weight: Theoretical: 5.834794 KDa

Sequence

String:

(DA)(DT)(DT)(DG)(DT)(DC)(DA)(DT)(DG)(DG) (DA)(DA)(DT)(DT)(DT)(DC)(DG)(DC)(DA)

Macromolecule #11: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.1 mg/mL
• Buffer: pH: 7 / Component - Concentration: 1.0 MM / Component - Name: DTT
• Grid: Model: C-flat-1/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM CPC / Details: 1 min incubation 3.5s blot.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Spherical aberration corrector: Microscope was modified with a Cs corrector (NeCEN netherlands)
• Image recording: Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 4916 / Average exposure time: 1.6 sec. / Average electron dose: 56.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 59000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 3125
• Startup model: Type of model: OTHER; Details: initial model based EMDB-2992 low pass filtered to 50A
• Final reconstruction: Number classes used: 3 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 177155
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.3)
• Final 3D classification: Number classes: 4 / Avg.num./class: 59000 / Software - Name: RELION (ver. 1.3); Details: Two rounds of 3D classification. First with 8 classes coarse sampling, second with 4 classes.

Atomic model buiding 1

Initial model

PDB ID	Chain
3utb	source_name: PDB, initial_model_type: experimental model
3os0	source_name: PDB, initial_model_type: experimental model

• Details: The initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine and namdinator. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix.
• Refinement: Space: REAL

Output model

PDB-6rny:
PFV intasome - nucleosome strand transfer complex