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- PDB-7a4t: Crystal structure of the GCN coiled-coil in complex with nanobody Nb39 -

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Basic information

Entry
Database: PDB / ID: 7a4t
TitleCrystal structure of the GCN coiled-coil in complex with nanobody Nb39
Components
  • GCN4 isoform 1
  • Nanobody Nb39
KeywordsDE NOVO PROTEIN / coiled-coil / nanobody / antibody / protein design
Function / homologyACETYL GROUP / :
Function and homology information
Biological speciesLama glama (llama)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.124 Å
AuthorsHadzi, S.
Funding supportEuropean Union, Slovenia, 3items
OrganizationGrant numberCountry
European Research Council (ERC)787115European Union
Slovenian Research AgencyP4-0176 Slovenia
Slovenian Research AgencyP1-0201 Slovenia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures.
Authors: Majerle, A. / Hadzi, S. / Aupic, J. / Satler, T. / Lapenta, F. / Strmsek, Z. / Lah, J. / Loris, R. / Jerala, R.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody Nb39
B: GCN4 isoform 1
C: GCN4 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0419
Polymers21,5513
Non-polymers4906
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-71 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.640, 106.640, 106.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-373-

HOH

31B-205-

HOH

41B-207-

HOH

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Components

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Antibody / Protein/peptide , 2 types, 3 molecules ABC

#1: Antibody Nanobody Nb39


Mass: 14783.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide GCN4 isoform 1


Mass: 3383.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZY2

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Non-polymers , 4 types, 103 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate 20 % w/v PEG 3350 / PH range: 7.2-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980127 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980127 Å / Relative weight: 1
ReflectionResolution: 2.124→47.691 Å / Num. obs: 12227 / % possible obs: 99.93 % / Redundancy: 20 % / Biso Wilson estimate: 41.61 Å2 / CC1/2: 1 / Rrim(I) all: 0.121 / Net I/σ(I): 27.45
Reflection shellResolution: 2.125→2.201 Å / Num. unique obs: 1177 / CC1/2: 0.859 / % possible all: 99.75

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modeler

Resolution: 2.124→47.691 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 612 5.01 %
Rwork0.1854 11615 -
obs0.1882 12227 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.54 Å2 / Biso mean: 53.3997 Å2 / Biso min: 24.37 Å2
Refinement stepCycle: final / Resolution: 2.124→47.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 27 97 1481
Biso mean--98.66 52.51 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081407
X-RAY DIFFRACTIONf_angle_d0.8721899
X-RAY DIFFRACTIONf_chiral_restr0.053207
X-RAY DIFFRACTIONf_plane_restr0.005244
X-RAY DIFFRACTIONf_dihedral_angle_d6.3361021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.124-2.33760.28641480.2239279999
2.3376-2.67590.26861500.2212853100
2.6759-3.37120.27181520.19852889100
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)
11.95960.3959-0.29641.7018-0.5315.51190.0258-0.14080.01880.0547-0.0291-0.15390.09220.27120.02070.25450.0143-0.02620.264-0.00680.300521.7445105.169127.942
24.53923.5201-4.11842.864-3.2313.88570.2486-0.9306-0.39440.4823-0.031-0.7814-0.30611.0166-0.41160.4707-0.0463-0.08390.6472-0.09070.529330.427109.4009149.5904
34.30220.0731-4.80855.82890.31765.42330.08050.29460.2842-0.1302-0.0657-0.3725-0.37310.6482-0.03880.4341-0.029-0.10660.7484-0.08370.380728.082108.5636141.3123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 121)A1 - 121
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 26)B0 - 26
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 27)C0 - 27

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