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- PDB-8slc: High Affinity nanobodies against GFP -

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Basic information

Entry
Database: PDB / ID: 8slc
TitleHigh Affinity nanobodies against GFP
Components
  • Green fluorescent protein
  • LaG43
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: 2.97 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 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: Green fluorescent protein
C: LaG43
D: LaG43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,49413
Polymers89,9614
Non-polymers5339
Water1629
1
C: LaG43
hetero molecules

A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2948
Polymers44,9802
Non-polymers3146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
2
B: Green fluorescent protein
hetero molecules

D: LaG43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2005
Polymers44,9802
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Unit cell
Length a, b, c (Å)149.435, 149.435, 127.013
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein Green fluorescent protein


Mass: 28794.396 Da / Num. of mol.: 2
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: Antibody LaG43


Mass: 16185.982 Da / Num. of mol.: 2
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, 18 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.55 Å3/Da / Density % sol: 72.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.6, 2 M sodium formate

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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: Jan 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. obs: 78984 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.117 / Χ2: 1.591 / Net I/σ(I): 9.4 / Num. measured all: 347306
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.91-2.974.40.64739190.9541100
2.97-3.044.40.52639621.0141100
3.04-3.124.40.37539351.0591100
3.12-3.24.40.33739941.0761100
3.2-3.34.40.25439041.1731100
3.3-3.44.40.20639631.2681100
3.4-3.524.40.17139401.4341100
3.52-3.664.40.13539491.62199.9
3.66-3.834.40.1239921.7881100
3.83-4.034.40.10439302.101199.9
4.03-4.294.40.08939642.5281100
4.29-4.624.30.07839533.026199.9
4.62-5.084.30.07139622.8881100
5.08-5.814.30.06539632.2621100
5.81-7.324.30.05939371.8621100
7.32-504.50.04339712.0891100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→48.91 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1655 5.02 %
Rwork0.2197 --
obs0.2208 32995 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.97→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 29 9 5638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065757
X-RAY DIFFRACTIONf_angle_d0.9497782
X-RAY DIFFRACTIONf_dihedral_angle_d8.877783
X-RAY DIFFRACTIONf_chiral_restr0.047821
X-RAY DIFFRACTIONf_plane_restr0.0071009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.060.2911380.31392619X-RAY DIFFRACTION100
3.06-3.160.30431370.29352612X-RAY DIFFRACTION100
3.16-3.270.30291400.29452637X-RAY DIFFRACTION100
3.27-3.40.32741370.28972593X-RAY DIFFRACTION100
3.4-3.550.23841390.26012626X-RAY DIFFRACTION99
3.55-3.740.29291400.24212616X-RAY DIFFRACTION99
3.74-3.980.28321380.24182584X-RAY DIFFRACTION99
3.98-4.280.231370.19932616X-RAY DIFFRACTION99
4.28-4.710.19781390.17412600X-RAY DIFFRACTION99
4.71-5.390.21431380.17552602X-RAY DIFFRACTION99
5.4-6.790.24771320.20252623X-RAY DIFFRACTION98
6.79-48.910.18811400.1952612X-RAY DIFFRACTION97

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