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- PDB-7eh3: Structure of Nanobody Nb23 in solution using NMR spectroscopy -

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Basic information

Entry
Database: PDB / ID: 7eh3
TitleStructure of Nanobody Nb23 in solution using NMR spectroscopy
ComponentsNb23
KeywordsIMMUNE SYSTEM / Single-domain antibody / antibody fragment
Biological speciesLama glama (llama)
MethodSOLUTION NMR / energy minimization
AuthorsPercipalle, M. / Hunashal, Y. / Esposito, G. / Fogolari, F.
Funding supportUnited Arab Emirates, 1items
OrganizationGrant numberCountry
Other private76 71260 ADHPG VP046United Arab Emirates
CitationJournal: Molecules / Year: 2021
Title: Structure of Nanobody Nb23.
Authors: Percipalle, M. / Hunashal, Y. / Steyaert, J. / Fogolari, F. / Esposito, G.
History
DepositionMar 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nb23


Theoretical massNumber of molelcules
Total (without water)15,2151
Polymers15,2151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Antibody Nb23


Mass: 15214.810 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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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
411isotropic12D 1H-15N HSQC
522isotropic12D 1H-15N TROSY
431isotropic13D CBCANH
441isotropic13D CBCA(CO)NH
451isotropic13D HNCA
461isotropic13D C(CO)NH
572isotropic13D H(CCO)NH
481isotropic13D HBHA(CO)NH
491isotropic13D HNCO
4101isotropic13D HN(CA)CO
6113isotropic12D 1H-1H TOCSY
5122isotropic13D 1H-15N NOESY
5135isotropic12D (HB)CB(CGCD)HD
5145isotropic12D (HB)CB(CGCDCE)HE
7154isotropic12D 1H-1H NOESY
5165isotropic13D 1H-13C NOESY aliphatic
5175isotropic13D 1H-13C NOESY aromatic
5182isotropic12D 1H-13C HSQC
5195isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride, 95% H2O/5% D2OSample_195% H2O/5% D2O
solution2290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2OSample_295% H2O/5% D2O
solution3190 uM Nb23, 10 mM sodium phosphate, 5 % D2O, 6.3 mM sodium chloride, 95% H2O/5% D2OSample_395% H2O/5% D2O
solution4100 uM Nb23, 10 mM sodium phosphate, 100 % D2O, 20 mM sodium chloride, 100% D2OSample_4100% D2O
solution5190 uM Nb23, 10 mM sodium phosphate, 100 % D2O, 100% D2OSample_5100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMNb23[U-10% 13C; U-100% 15N]1
10 mMsodium phosphatenatural abundance1
5 %D2Onatural abundance1
19.5 mMTRISnatural abundance1
21 mMsodium chloridenatural abundance1
290 uMNb23[U-10% 13C; U-100% 15N]2
10 mMsodium phosphatenatural abundance2
5 %D2Onatural abundance2
190 uMNb23natural abundance3
10 mMsodium phosphatenatural abundance3
5 %D2Onatural abundance3
6.3 mMsodium chloridenatural abundance3
100 uMNb23natural abundance4
10 mMsodium phosphatenatural abundance4
100 %D2Onatural abundance4
20 mMsodium chloridenatural abundance4
190 uMNb23natural abundance5
10 mMsodium phosphatenatural abundance5
100 %D2Onatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
421 (sodium chloride) mMconditions_16.95 1 atm298 K
50 mMconditions_26.95 1 atm298 K
66.3 mMconditions_36.95 1 atm298 K
720 mMconditions_46.95 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift calculation
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
MolProbityRichardsongeometry optimization
MolProbityRichardsondata analysis
PONDEROSALee W, Kim JH, Westler WM, Markley JLdata analysis
PONDEROSALee W, Kim JH, Westler WM, Markley JLrefinement
PONDEROSALee W, Kim JH, Westler WM, Markley JLstructure calculation
PONDEROSALee W, Kim JH, Westler WM, Markley JLgeometry optimization
PONDEROSA-C/SLee W, Stark JL, Markley JLrefinement
PONDEROSA-C/SLee W, Stark JL, Markley JLstructure calculation
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntongeometry optimization
PyMOLThe PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLCgeometry optimization
PyMOLThe PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLCdata analysis
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
TALOS-NYang S, Bax Ageometry optimization
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
NAMDNAMD2Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shi- nozaki A, Varadarajan K, Schulten Krefinement
RefinementMethod: energy minimization / Software ordinal: 22
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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