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- PDB-5uea: Structure of antigen-Fab complex with Histone chaperone ASF1 -

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Basic information

Entry
Database: PDB / ID: 5uea
TitleStructure of antigen-Fab complex with Histone chaperone ASF1
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
KeywordsIMMUNE SYSTEM / Antibody / Fab / Asf1 / histone 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 / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsBailey, L.J. / Kossiakoff, A.A.
Citation
Journal: To Be Published
Title: Antibody Switch Residue Engineering for Improved Crystallization Chaperones
Authors: Bailey, L.J. / Kossiakoff, A.A.
#1: Journal: To Be Published
Title: To be published
Authors: Bailey, L.J. / Kossiakoff, A.A.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
X: Histone chaperone ASF1
H: Fab Heavy Chain
D: Histone chaperone ASF1
L: Fab Light Chain
B: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)130,6326
Polymers130,6326
Non-polymers00
Water19,4561080
1
A: Fab Heavy Chain
X: Histone chaperone ASF1
B: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)65,3163
Polymers65,3163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area25510 Å2
MethodPISA
2
H: Fab Heavy Chain
D: Histone chaperone ASF1
L: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)65,3163
Polymers65,3163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-34 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.561, 81.770, 82.150
Angle α, β, γ (deg.)70.51, 77.28, 81.67
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab Heavy Chain


Mass: 24428.393 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.: 1080 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, .2 M Ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.701→39.347 Å / Num. obs: 133679 / % possible obs: 96.97 % / Redundancy: 2.2 % / Net I/σ(I): 8.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.701→39.347 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.7
RfactorNum. reflection% reflection
Rfree0.2073 6727 5.03 %
Rwork0.1539 --
obs0.1566 133671 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→39.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8695 0 0 1080 9775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068909
X-RAY DIFFRACTIONf_angle_d0.85212158
X-RAY DIFFRACTIONf_dihedral_angle_d5.3075299
X-RAY DIFFRACTIONf_chiral_restr0.0541392
X-RAY DIFFRACTIONf_plane_restr0.0051549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7005-1.71990.2982020.22594033X-RAY DIFFRACTION92
1.7199-1.74010.29972050.20494208X-RAY DIFFRACTION96
1.7401-1.76130.26822200.19964114X-RAY DIFFRACTION96
1.7613-1.78360.2942230.19174263X-RAY DIFFRACTION97
1.7836-1.80710.28772190.18274165X-RAY DIFFRACTION95
1.8071-1.83180.2292180.17334158X-RAY DIFFRACTION96
1.8318-1.8580.23682330.16574281X-RAY DIFFRACTION96
1.858-1.88580.23552130.16474154X-RAY DIFFRACTION96
1.8858-1.91520.26032200.15884231X-RAY DIFFRACTION97
1.9152-1.94660.21862250.15794232X-RAY DIFFRACTION96
1.9466-1.98020.23912200.15674206X-RAY DIFFRACTION97
1.9802-2.01620.23592310.15824235X-RAY DIFFRACTION97
2.0162-2.0550.22092370.154236X-RAY DIFFRACTION97
2.055-2.09690.22422290.15024233X-RAY DIFFRACTION97
2.0969-2.14250.22611970.14654222X-RAY DIFFRACTION97
2.1425-2.19230.21562270.15144250X-RAY DIFFRACTION97
2.1923-2.24720.21042400.14734231X-RAY DIFFRACTION98
2.2472-2.30790.22692410.1484230X-RAY DIFFRACTION97
2.3079-2.37580.20912560.14874243X-RAY DIFFRACTION98
2.3758-2.45250.22342180.15014261X-RAY DIFFRACTION98
2.4525-2.54010.22682230.15724292X-RAY DIFFRACTION98
2.5401-2.64180.21692180.15284312X-RAY DIFFRACTION98
2.6418-2.7620.20512080.16114264X-RAY DIFFRACTION98
2.762-2.90760.21332270.16214294X-RAY DIFFRACTION98
2.9076-3.08970.20432480.16034285X-RAY DIFFRACTION98
3.0897-3.32810.19712310.15194280X-RAY DIFFRACTION99
3.3281-3.66280.19622080.14644307X-RAY DIFFRACTION98
3.6628-4.19230.18832320.14344290X-RAY DIFFRACTION99
4.1923-5.27990.15692210.12844290X-RAY DIFFRACTION98
5.2799-39.35760.17632370.16594144X-RAY DIFFRACTION95

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