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- PDB-9awe: The crystal structure of an engineered Protein GF with Human Kappa Fab -

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Basic information

Entry
Database: PDB / ID: 9awe
TitleThe crystal structure of an engineered Protein GF with Human Kappa Fab
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Histone chaperone ASF1
  • Immunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / antibody / protein G / Fab / ASF1 / Histone chaperone
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 / IgG binding / silent mating-type cassette heterochromatin formation / cellular response to stress / negative regulation of DNA damage checkpoint / subtelomeric heterochromatin formation ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / H3 histone acetyltransferase complex / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / nucleosome disassembly / IgG binding / 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 / extracellular region / nucleus / cytosol
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily ...Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Histone chaperone ASF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 5, 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: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)72,9114
Polymers72,9114
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.869, 85.660, 180.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: 18244.432 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: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 7090.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Cacodylate pH 6.0, 0.1M Calcium acetate hydrate, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→90.05 Å / Num. obs: 21810 / % possible obs: 97.38 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2203 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→90.05 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2927 1095 5.03 %
Rwork0.2503 --
obs0.2526 21781 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→90.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 14 4822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096710
X-RAY DIFFRACTIONf_angle_d1.2096710
X-RAY DIFFRACTIONf_dihedral_angle_d6.582678
X-RAY DIFFRACTIONf_chiral_restr0.065769
X-RAY DIFFRACTIONf_plane_restr0.009858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.39711280.35482597X-RAY DIFFRACTION97
2.93-3.080.35411370.33542537X-RAY DIFFRACTION96
3.08-3.270.39421360.31552513X-RAY DIFFRACTION94
3.27-3.530.38171320.29162624X-RAY DIFFRACTION98
3.53-3.880.32531360.25992601X-RAY DIFFRACTION96
3.88-4.440.26851370.22872548X-RAY DIFFRACTION94
4.44-5.60.251480.20782609X-RAY DIFFRACTION96
5.6-90.050.23641410.22052657X-RAY DIFFRACTION92
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)
11.15770.04540.51860.45310.74361.66720.2435-0.31990.08170.10680.0149-0.0208-0.2015-0.40150.1681.12140.09260.40280.5236-0.03750.4116.59219.53830.617
20.4952-0.3449-0.09770.26420.24071.61670.3684-0.2259-0.050.3312-0.13090.36280.206-0.7322-0.20321.0212-0.18790.24430.61820.03360.462311.2172.86327.165
30.7519-0.7523-0.95961.43310.22032.60080.26230.16530.2063-0.6209-0.02660.1179-1.2473-0.10740.01151.92310.14010.20340.5339-0.00820.481719.67426.539-10.482
46.1035-4.19621.33974.10750.66747.21740.409-0.59240.53060.694-0.165-0.1764-0.8412-0.9506-0.22511.612-0.30910.29050.8726-0.11640.690417.44826.33157.963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 2:219 )B2 - 219
2X-RAY DIFFRACTION2( CHAIN D AND RESID 4:212 )D4 - 212
3X-RAY DIFFRACTION3( CHAIN A AND RESID 2:154 )A2 - 154
4X-RAY DIFFRACTION4( CHAIN C AND RESID 10:63 )C10 - 63

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