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- PDB-8pe1: Crystal structure of Gel4 in complex with Nanobody 4 -

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Basic information

Entry
Database: PDB / ID: 8pe1
TitleCrystal structure of Gel4 in complex with Nanobody 4
Components
  • 1,3-beta-glucanosyltransferase
  • Nanobody 4
KeywordsTRANSFERASE / Transglycosylase / b-1 / 3-glucan / nanobodies / fungal diseases
Function / homology
Function and homology information


1,3-beta-glucanosyltransferase activity / fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process / fungal-type cell wall organization / fungal-type cell wall / Transferases; Glycosyltransferases; Hexosyltransferases / side of membrane / vesicle / plasma membrane
Similarity search - Function
Glucanosyltransferase / Glucanosyltransferase / X8 domain / X8 domain / Possibly involved in carbohydrate binding / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / 1,3-beta-glucanosyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMacias-Leon, J. / Redrado-Hernandez, S. / Castro-Lopez, J. / Sanz, A.B. / Arias, M. / Farkas, V. / Vincke, C. / Muyldermans, S. / Pardo, J. / Arroyo, J. ...Macias-Leon, J. / Redrado-Hernandez, S. / Castro-Lopez, J. / Sanz, A.B. / Arias, M. / Farkas, V. / Vincke, C. / Muyldermans, S. / Pardo, J. / Arroyo, J. / Galvez, E. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Broad Protection against Invasive Fungal Disease from a Nanobody Targeting the Active Site of Fungal beta-1,3-Glucanosyltransferases.
Authors: Redrado-Hernandez, S. / Macias-Leon, J. / Castro-Lopez, J. / Belen Sanz, A. / Dolader, E. / Arias, M. / Gonzalez-Ramirez, A.M. / Sanchez-Navarro, D. / Petryk, Y. / Farkas, V. / Vincke, C. / ...Authors: Redrado-Hernandez, S. / Macias-Leon, J. / Castro-Lopez, J. / Belen Sanz, A. / Dolader, E. / Arias, M. / Gonzalez-Ramirez, A.M. / Sanchez-Navarro, D. / Petryk, Y. / Farkas, V. / Vincke, C. / Muyldermans, S. / Garcia-Barbazan, I. / Del Agua, C. / Zaragoza, O. / Arroyo, J. / Pardo, J. / Galvez, E.M. / Hurtado-Guerrero, R.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Aug 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 1,3-beta-glucanosyltransferase
A: 1,3-beta-glucanosyltransferase
C: Nanobody 4
D: Nanobody 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,93424
Polymers128,0854
Non-polymers3,84920
Water12,412689
1
B: 1,3-beta-glucanosyltransferase
D: Nanobody 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,96712
Polymers64,0432
Non-polymers1,92510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 1,3-beta-glucanosyltransferase
C: Nanobody 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,96712
Polymers64,0432
Non-polymers1,92510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.388, 86.330, 178.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUBA18 - 4661 - 449
21ALAALALEULEUAB18 - 4661 - 449
12GLNGLNALAALACC1 - 1241 - 124
22GLNGLNALAALADD1 - 1241 - 124

NCS ensembles :
ID
1
2

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Components

#1: Protein 1,3-beta-glucanosyltransferase


Mass: 50267.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: CDV57_08969 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A229W401
#2: Antibody Nanobody 4


Mass: 13775.122 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Halogens, buffer system 3, P500MME P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→20.01 Å / Num. obs: 104001 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.182 / Net I/σ(I): 6
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 1.588 / Mean I/σ(I) obs: 1 / Num. unique obs: 15033 / CC1/2: 0.537

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W62

2w62


Resolution: 1.9→20.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.214 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26446 4072 3.9 %RANDOM
Rwork0.21537 ---
obs0.21726 99854 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.531 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--3.39 Å20 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8826 0 238 689 9753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139309
X-RAY DIFFRACTIONr_bond_other_d0.0010.0188068
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.68512644
X-RAY DIFFRACTIONr_angle_other_deg1.3341.61418863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04451144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54823.795477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.094151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7761540
X-RAY DIFFRACTIONr_chiral_restr0.0720.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021912
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.212.9944567
X-RAY DIFFRACTIONr_mcbond_other2.2092.9934566
X-RAY DIFFRACTIONr_mcangle_it3.324.4715696
X-RAY DIFFRACTIONr_mcangle_other3.3214.4725697
X-RAY DIFFRACTIONr_scbond_it3.2433.3114742
X-RAY DIFFRACTIONr_scbond_other3.2383.3114742
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0194.8446943
X-RAY DIFFRACTIONr_long_range_B_refined6.48335.55410499
X-RAY DIFFRACTIONr_long_range_B_other6.43935.32110376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B141800.07
12A141800.07
21C38340.08
22D38340.08
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 305 -
Rwork0.379 7280 -
obs--99.72 %

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