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- PDB-9avo: The crystal structure of an engineered Protein GD with Human Kappa Fab -

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Basic information

Entry
Database: PDB / ID: 9avo
TitleThe crystal structure of an engineered Protein GD with Human Kappa Fab
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
  • Protein GD
KeywordsIMMUNE SYSTEM/Chaperone / Fab / Antibody / Protein G / Immunoglobulin Binding Protein / ASF1 / IMMUNE SYSTEM-Chaperone complex
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / 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 / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / 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 deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone
Similarity search - Domain/homology
Histone chaperone ASF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSlezak, T. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117372 United States
CitationJournal: Protein Sci. / Year: 2025
Title: Engineered protein G variants for multifunctional antibody-based assemblies.
Authors: Slezak, T. / O'Leary, K.M. / Li, J. / Rohaim, A. / Davydova, E.K. / Kossiakoff, A.A.
History
DepositionMar 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fab Heavy Chain
D: Fab Light Chain
A: Histone chaperone ASF1
C: Protein GD


Theoretical massNumber of molelcules
Total (without water)73,2064
Polymers73,2064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-39 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.971, 134.971, 339.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Antibody Fab Heavy Chain


Mass: 24177.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#2: Antibody Fab Light Chain


Mass: 23397.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Protein Histone chaperone ASF1 / Anti-silencing function protein 1 / yASF1


Mass: 18516.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1, CIA1, YJL115W, J0755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32447
#4: Protein Protein GD


Mass: 7113.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: 5.45 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Sodium cacodylate pH 6.8 and 0.8M Sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→86.73 Å / Num. obs: 31838 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 80.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.049 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 13 % / Num. unique obs: 4540 / CC1/2: 0.879 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→86.73 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1619 5.1 %
Rwork0.2145 --
obs0.2158 31735 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→86.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4912 0 0 0 4912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01730
X-RAY DIFFRACTIONf_angle_d1.28690
X-RAY DIFFRACTIONf_dihedral_angle_d6.469691
X-RAY DIFFRACTIONf_chiral_restr0.067791
X-RAY DIFFRACTIONf_plane_restr0.012873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.090.43631130.38922465X-RAY DIFFRACTION99
3.09-3.190.41281380.35172452X-RAY DIFFRACTION100
3.19-3.30.36631430.34392465X-RAY DIFFRACTION99
3.3-3.430.33141230.29372467X-RAY DIFFRACTION99
3.43-3.590.28981330.25542479X-RAY DIFFRACTION100
3.59-3.780.23751210.23992505X-RAY DIFFRACTION100
3.78-4.020.30091510.22922495X-RAY DIFFRACTION100
4.02-4.330.16911380.1842516X-RAY DIFFRACTION100
4.33-4.760.17931130.14362513X-RAY DIFFRACTION99
4.76-5.450.18111380.15442540X-RAY DIFFRACTION100
5.45-6.870.24651320.19842556X-RAY DIFFRACTION99
6.87-86.730.21511760.20192663X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.2028 Å / Origin y: -8.148 Å / Origin z: 25.401 Å
111213212223313233
T0.8735 Å2-0.0042 Å2-0.1767 Å2-0.5093 Å2-0.0022 Å2--0.8233 Å2
L1.5043 °2-0.0279 °2-0.3516 °2-0.7522 °20.0459 °2--3.0029 °2
S-0.0306 Å °-0.0721 Å °0.009 Å °0.425 Å °0.1165 Å °-0.1194 Å °0.2593 Å °0.7983 Å °-0.0826 Å °
Refinement TLS groupSelection details: all

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