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- PDB-6az2: Crystal structure of Asf1-Fab 12E complex -

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Basic information

Entry
Database: PDB / ID: 6az2
TitleCrystal structure of Asf1-Fab 12E complex
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
KeywordsIMMUNE SYSTEM / Antibody / Complex / Asf1 / Crystal Chaperone
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / protein modification process / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / chromosome, telomeric region / regulation of transcription by RNA polymerase II / chromatin / nucleus / cytosol
Similarity search - Function
Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.477 Å
AuthorsBailey, L.J. / Kossiakoff, A.A.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.
Authors: Bailey, L.J. / Sheehy, K.M. / Dominik, P.K. / Liang, W.G. / Rui, H. / Clark, M. / Jaskolowski, M. / Kim, Y. / Deneka, D. / Tang, W.J. / Kossiakoff, A.A.
History
DepositionSep 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Heavy Chain
C: Fab Heavy Chain
B: Histone chaperone ASF1
D: Histone chaperone ASF1
E: Fab Light Chain
F: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)130,5886
Polymers130,5886
Non-polymers00
Water4,756264
1
A: Fab Heavy Chain
B: Histone chaperone ASF1
F: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)65,2943
Polymers65,2943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area25110 Å2
MethodPISA
2
C: Fab Heavy Chain
D: Histone chaperone ASF1
E: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)65,2943
Polymers65,2943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-35 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.666, 109.743, 122.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab Heavy Chain


Mass: 24406.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 17428.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ASF1, CIA1, YJL115W, J0755 / Production host: Escherichia coli (E. coli) / References: UniProt: P32447
#3: Antibody Fab Light Chain


Mass: 23459.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 20% PEG3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.477→50.055 Å / Num. obs: 47748 / % possible obs: 98.7611 % / Redundancy: 3.4 % / Net I/σ(I): 30.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-3000data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.477→50.055 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2276 2416 5.06 %
Rwork0.1931 --
obs0.1948 47748 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.477→50.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8686 0 0 264 8950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038897
X-RAY DIFFRACTIONf_angle_d0.64312123
X-RAY DIFFRACTIONf_dihedral_angle_d10.4695315
X-RAY DIFFRACTIONf_chiral_restr0.0471378
X-RAY DIFFRACTIONf_plane_restr0.0041543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4772-2.52770.30961030.25312164X-RAY DIFFRACTION80
2.5277-2.58270.30071390.24292646X-RAY DIFFRACTION100
2.5827-2.64280.3151560.23822656X-RAY DIFFRACTION100
2.6428-2.70880.27511550.23762656X-RAY DIFFRACTION100
2.7088-2.78210.28061550.25852652X-RAY DIFFRACTION100
2.7821-2.86390.29921360.23582663X-RAY DIFFRACTION100
2.8639-2.95640.28911410.22592675X-RAY DIFFRACTION100
2.9564-3.0620.24881150.22952714X-RAY DIFFRACTION100
3.062-3.18460.26171510.22532651X-RAY DIFFRACTION100
3.1846-3.32950.24731460.22282683X-RAY DIFFRACTION100
3.3295-3.5050.2251240.20352721X-RAY DIFFRACTION100
3.505-3.72450.23391530.18962684X-RAY DIFFRACTION100
3.7245-4.0120.22171590.17952690X-RAY DIFFRACTION100
4.012-4.41550.18361230.15582728X-RAY DIFFRACTION100
4.4155-5.05390.15961590.13532728X-RAY DIFFRACTION100
5.0539-6.36540.18551690.1562737X-RAY DIFFRACTION100
6.3654-50.06480.22251320.192884X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8029-0.20731.72140.1897-0.87353.71470.12940.25530.0217-0.3301-0.1890.05110.40520.36320.04110.48440.1207-0.04450.3812-0.00370.3724-7.198342.0305-49.4162
23.2372-0.11251.30810.79290.05351.5146-0.0374-0.1265-0.0828-0.08550.02530.22890.0561-0.41410.00450.2544-0.05280.0250.40570.0170.3121-39.642724.9526-14.9029
33.31461.2466-0.19762.191-0.25152.6609-0.1317-0.180.2270.038-0.1431-0.1346-0.34560.45090.2330.3013-0.0101-0.06790.2870.05720.32533.774148.8401-10.4403
41.3159-0.1781-0.07051.98-1.07854.20820.1061-0.1672-0.14690.04730.02670.13330.2642-0.0541-0.10660.1937-0.0314-0.01990.188-0.01520.2863-0.034415.5514-5.5196
52.74640.06431.23330.4271-0.15121.68570.0230.5316-0.3277-0.31710.08360.1162-0.0325-0.1518-0.10180.4432-0.032-0.06630.4619-0.09290.3637-36.009217.7934-31.7107
60.63260.37321.25620.39740.89724.18090.0708-0.0422-0.0245-0.2508-0.12120.1361-0.0264-0.61850.06530.41270.0828-0.0680.38420.01290.3961-24.323148.9416-46.2672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:217)
2X-RAY DIFFRACTION2(chain C and resseq 1:218)
3X-RAY DIFFRACTION3(chain B and resseq 2:154)
4X-RAY DIFFRACTION4(chain D and resseq 2:154)
5X-RAY DIFFRACTION5(chain E and resseq 3:212)
6X-RAY DIFFRACTION6(chain F and resseq 3:213)

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