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

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Basic information

Entry
Database: PDB / ID: 6ayz
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 / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II ...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 / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / protein modification process / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / chromatin / regulation of transcription by RNA polymerase II / 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: 2.096 Å
AuthorsBailey, L.J. / Kossiakoff, A.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094588 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117372 United States
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 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fab Heavy Chain
C: Fab Light Chain
D: Fab Light Chain
M: Histone chaperone ASF1
R: Fab Heavy Chain
A: Histone chaperone ASF1


Theoretical massNumber of molelcules
Total (without water)128,9866
Polymers128,9866
Non-polymers00
Water13,313739
1
B: Fab Heavy Chain
D: Fab Light Chain
A: Histone chaperone ASF1


Theoretical massNumber of molelcules
Total (without water)64,4933
Polymers64,4933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-33 kcal/mol
Surface area25420 Å2
MethodPISA
2
C: Fab Light Chain
M: Histone chaperone ASF1
R: Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)64,4933
Polymers64,4933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-39 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.811, 77.445, 101.734
Angle α, β, γ (deg.)90.00, 110.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab Heavy Chain


Mass: 23708.410 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: Antibody Fab Light Chain


Mass: 23355.900 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)
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 0.2 M Ammonium Acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.096→35.952 Å / Num. obs: 73866 / % possible obs: 99.39 % / Redundancy: 3.5 % / Net I/σ(I): 32.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.096→35.952 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 3712 5.03 %
Rwork0.1914 --
obs0.1937 73866 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.096→35.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8889 0 0 739 9628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049120
X-RAY DIFFRACTIONf_angle_d0.66612442
X-RAY DIFFRACTIONf_dihedral_angle_d11.0835434
X-RAY DIFFRACTIONf_chiral_restr0.0471413
X-RAY DIFFRACTIONf_plane_restr0.0041591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0958-2.12240.27091220.2422275X-RAY DIFFRACTION87
2.1224-2.15030.31091480.2352594X-RAY DIFFRACTION100
2.1503-2.17970.29171370.23272561X-RAY DIFFRACTION100
2.1797-2.21090.27331250.23122637X-RAY DIFFRACTION100
2.2109-2.24390.25231390.22712580X-RAY DIFFRACTION100
2.2439-2.27890.2991140.23522638X-RAY DIFFRACTION100
2.2789-2.31630.26981480.22912551X-RAY DIFFRACTION100
2.3163-2.35620.33261230.22852621X-RAY DIFFRACTION100
2.3562-2.3990.29121440.23682574X-RAY DIFFRACTION100
2.399-2.44520.2971070.2272626X-RAY DIFFRACTION100
2.4452-2.49510.28221430.22522640X-RAY DIFFRACTION100
2.4951-2.54930.29471250.22392596X-RAY DIFFRACTION100
2.5493-2.60860.2621480.22562603X-RAY DIFFRACTION100
2.6086-2.67380.281560.22022586X-RAY DIFFRACTION100
2.6738-2.74610.25631310.22282585X-RAY DIFFRACTION100
2.7461-2.82690.26951410.21392632X-RAY DIFFRACTION100
2.8269-2.91810.34621340.22772608X-RAY DIFFRACTION100
2.9181-3.02230.26771320.22782614X-RAY DIFFRACTION100
3.0223-3.14320.24621440.21732594X-RAY DIFFRACTION100
3.1432-3.28620.25981270.20552647X-RAY DIFFRACTION100
3.2862-3.45930.25471440.20782601X-RAY DIFFRACTION100
3.4593-3.67590.20781540.1842607X-RAY DIFFRACTION100
3.6759-3.95940.22761390.1762609X-RAY DIFFRACTION100
3.9594-4.35720.21471590.15922597X-RAY DIFFRACTION100
4.3572-4.98630.16491400.12822638X-RAY DIFFRACTION100
4.9863-6.27670.17341440.15562639X-RAY DIFFRACTION100
6.2767-35.95770.18681440.15122701X-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)
12.7072-0.26850.53240.2478-0.00120.41680.0893-0.1981-0.05160.0011-0.0047-0.0090.0373-0.1105-0.0830.3124-0.03550.00850.22510.01460.235638.0748.20494.3028
22.6530.08530.72810.1881-0.08161.13690.0057-0.3301-0.2119-0.01670.09060.07540.2172-0.3781-0.09560.2966-0.0525-0.01090.31890.04580.24842.5308-2.842644.6722
32.676-0.58550.94310.342-0.20480.71880.00140.221-0.29940.01120.03520.01620.05940.109-0.05340.2464-0.00880.00540.1805-0.02360.225643.6496-0.757479.6425
41.48240.04860.44091.7982-0.72621.9989-0.04030.15830.1393-0.00510.0132-0.1029-0.15190.14690.03820.1883-0.0219-0.00670.27670.00080.238946.81332.765945.1047
53.0398-0.16910.47310.6323-0.05890.8920.05660.03260.0537-0.0064-0.03010.06540.0314-0.0882-0.03160.277-0.02720.00680.21740.0120.21798.18920.828.3003
63.2693-0.79620.74682.7191-0.67592.53630.12190.20550.11490.0181-0.11340.0413-0.0458-0.0171-0.01470.17830.01770.02290.25570.00020.2392-0.31969.576275.9734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resseq 0:219)
2X-RAY DIFFRACTION2(chain C and resseq 2:211)
3X-RAY DIFFRACTION3(chain D and resseq 2:212)
4X-RAY DIFFRACTION4(chain M and resseq 9:153)
5X-RAY DIFFRACTION5(chain R and resseq 1:221)
6X-RAY DIFFRACTION6(chain A and resseq 9:154)

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