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- PDB-8sfv: High affinity nanobodies to GFP -

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Basic information

Entry
Database: PDB / ID: 8sfv
TitleHigh affinity nanobodies to GFP
Components
  • Green fluorescent protein
  • LaG19
KeywordsIMMUNE SYSTEM / Nanobody / nanobodies / GFP / green fluorescent protein / high-affinity antibody variant / antibody variant / single-domain antibody
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsKetaren, N.E. / Rout, M.P. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2025
Title: Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies.
Authors: Ketaren, N.E. / Fridy, P.C. / Malashkevich, V. / Sanyal, T. / Brillantes, M. / Thompson, M.K. / Oren, D.A. / Bonanno, J.B. / Sali, A. / Almo, S.C. / Chait, B.T. / Rout, M.P.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: LaG19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,35121
Polymers44,3422
Non-polymers1,00919
Water3,063170
1
A: Green fluorescent protein
hetero molecules

B: LaG19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,35121
Polymers44,3422
Non-polymers1,00919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-y-1/2,x,z-1/41
Unit cell
Length a, b, c (Å)111.251, 111.251, 193.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-307-

NA

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Green fluorescent protein


Mass: 28794.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Protein LaG19


Mass: 15547.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 189 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulphate, 0.1 M tris pH 7.0, 1 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 107447 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Χ2: 1.652 / Net I/σ(I): 9.8 / Num. measured all: 805788
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.83-1.867.50.8853550.8031100
1.86-1.97.60.76653730.7971100
1.9-1.947.60.59154040.8511100
1.94-1.987.60.46654080.8711100
1.98-2.037.60.37854010.9131100
2.03-2.087.60.30553740.9671100
2.08-2.137.60.25353991.0421100
2.13-2.27.60.21553711.1341100
2.2-2.277.60.18154201.2021100
2.27-2.357.60.16353611.2531100
2.35-2.447.60.14254151.3521100
2.44-2.557.70.12553761.511100
2.55-2.697.70.10953841.6921100
2.69-2.867.60.09654221.9121100
2.86-3.087.60.08353742.4181100
3.08-3.397.40.07454083.2561100
3.39-3.887.20.06553843.6481100
3.88-4.8870.05453983.5291100
4.88-507.40.05353913.347199.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→41.25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1921 3.7 %
Rwork0.1827 --
obs0.1835 51900 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 54 170 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112909
X-RAY DIFFRACTIONf_angle_d1.153928
X-RAY DIFFRACTIONf_dihedral_angle_d10.891396
X-RAY DIFFRACTIONf_chiral_restr0.065416
X-RAY DIFFRACTIONf_plane_restr0.01506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.31921210.29193146X-RAY DIFFRACTION86
1.88-1.930.29161250.26523273X-RAY DIFFRACTION90
1.93-1.980.27241300.23233382X-RAY DIFFRACTION92
1.98-2.050.2361340.21733469X-RAY DIFFRACTION95
2.05-2.120.24381350.20513523X-RAY DIFFRACTION97
2.12-2.210.21821380.20723569X-RAY DIFFRACTION97
2.21-2.310.2241380.21653585X-RAY DIFFRACTION98
2.31-2.430.26051380.20853611X-RAY DIFFRACTION99
2.43-2.580.24141400.19983644X-RAY DIFFRACTION99
2.58-2.780.23091410.20413671X-RAY DIFFRACTION99
2.78-3.060.20971420.22253686X-RAY DIFFRACTION100
3.06-3.50.21731430.18463723X-RAY DIFFRACTION100
3.5-4.410.17021450.14073767X-RAY DIFFRACTION100
4.41-41.250.16571510.14973930X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.7565 Å / Origin y: -19.2387 Å / Origin z: -23.0215 Å
111213212223313233
T0.1837 Å2-0.0354 Å2-0.015 Å2-0.5526 Å20.1727 Å2--0.4253 Å2
L-1.1141 °20.0551 °2-0.1018 °2-1.4125 °2-0.8703 °2--1.5017 °2
S-0.0738 Å °-0.1367 Å °-0.1118 Å °-0.0831 Å °0.0543 Å °0.0287 Å °0.2144 Å °-0.0188 Å °0.0256 Å °
Refinement TLS groupSelection details: all

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