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- PDB-7a4y: Crystal structure of the P5P6 coiled-coil in complex with nanobod... -

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Basic information

Entry
Database: PDB / ID: 7a4y
TitleCrystal structure of the P5P6 coiled-coil in complex with nanobody Nb34.
Components
  • Coiled-coil P5 peptide
  • Coiled-coil P6 peptide
  • Nanobody Nb34
KeywordsDE NOVO PROTEIN / coiled-coil / nanobody / antibody / protein design
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.157 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 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 16, 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
A: Nanobody Nb34
B: Nanobody Nb34
C: Nanobody Nb34
D: Coiled-coil P6 peptide
E: Coiled-coil P5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,84313
Polymers51,1425
Non-polymers7018
Water2,324129
1
A: Nanobody Nb34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8633
Polymers14,7051
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody Nb34
D: Coiled-coil P6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4945
Polymers18,2402
Non-polymers2543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nanobody Nb34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8973
Polymers14,7051
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Coiled-coil P5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5882
Polymers3,4921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.450, 72.450, 193.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 16 or resid 18...
21(chain B and (resid 3 through 16 or resid 18...
31(chain C and (resid 3 through 16 or resid 18...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLY(chain A and (resid 3 through 16 or resid 18...AA3 - 163 - 16
12LEULEUPHEPHE(chain A and (resid 3 through 16 or resid 18...AA18 - 2918 - 29
13ASPASPVALVAL(chain A and (resid 3 through 16 or resid 18...AA32 - 4832 - 48
14GLNGLNSERSER(chain A and (resid 3 through 16 or resid 18...AA3 - 1153 - 115
15GLNGLNSERSER(chain A and (resid 3 through 16 or resid 18...AA3 - 1153 - 115
16GLNGLNSERSER(chain A and (resid 3 through 16 or resid 18...AA3 - 1153 - 115
17GLNGLNSERSER(chain A and (resid 3 through 16 or resid 18...AA3 - 1153 - 115
18GLNGLNSERSER(chain A and (resid 3 through 16 or resid 18...AA3 - 1153 - 115
19GLNGLNSERSER(chain A and (resid 3 through 16 or resid 18...AA3 - 1153 - 115
21GLNGLNGLYGLY(chain B and (resid 3 through 16 or resid 18...BB3 - 163 - 16
22LEULEUSERSER(chain B and (resid 3 through 16 or resid 18...BB18 - 2518 - 25
23GLNGLNVALVAL(chain B and (resid 3 through 16 or resid 18...BB26 - 226 - 2
24VALVALARGARG(chain B and (resid 3 through 16 or resid 18...BB2 - 1172 - 117
25VALVALARGARG(chain B and (resid 3 through 16 or resid 18...BB2 - 1172 - 117
26VALVALARGARG(chain B and (resid 3 through 16 or resid 18...BB2 - 1172 - 117
27VALVALARGARG(chain B and (resid 3 through 16 or resid 18...BB2 - 1172 - 117
31GLNGLNGLYGLY(chain C and (resid 3 through 16 or resid 18...CC3 - 163 - 16
32LEULEUSERSER(chain C and (resid 3 through 16 or resid 18...CC18 - 2518 - 25
33GLNGLNPHEPHE(chain C and (resid 3 through 16 or resid 18...CC26 - 2726 - 27
34VALVALSERSER(chain C and (resid 3 through 16 or resid 18...CC2 - 1152 - 115
35VALVALSERSER(chain C and (resid 3 through 16 or resid 18...CC2 - 1152 - 115
36VALVALSERSER(chain C and (resid 3 through 16 or resid 18...CC2 - 1152 - 115
37VALVALSERSER(chain C and (resid 3 through 16 or resid 18...CC2 - 1152 - 115

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Components

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Protein/peptide , 2 types, 2 molecules DE

#2: Protein/peptide Coiled-coil P6 peptide


Mass: 3534.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Coiled-coil P5 peptide


Mass: 3491.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 1 types, 3 molecules ABC

#1: Antibody Nanobody Nb34


Mass: 14705.212 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 3 types, 137 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulphate, Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980126 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: 0.980126 Å / Relative weight: 1
ReflectionResolution: 2.157→45.008 Å / Num. obs: 32518 / % possible obs: 99.39 % / Redundancy: 11 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.122 / Net I/σ(I): 14.99
Reflection shellResolution: 2.157→2.234 Å / Num. unique obs: 3060 / CC1/2: 0.853 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

Resolution: 2.157→45.008 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1622 5 %
Rwork0.1961 30847 -
obs0.1977 32469 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.03 Å2 / Biso mean: 56.659 Å2 / Biso min: 27.97 Å2
Refinement stepCycle: final / Resolution: 2.157→45.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 38 129 3172
Biso mean--92.8 54.05 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083119
X-RAY DIFFRACTIONf_angle_d1.0114212
X-RAY DIFFRACTIONf_chiral_restr0.058447
X-RAY DIFFRACTIONf_plane_restr0.006547
X-RAY DIFFRACTIONf_dihedral_angle_d9.1412184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1402X-RAY DIFFRACTION12.26TORSIONAL
12B1402X-RAY DIFFRACTION12.26TORSIONAL
13C1402X-RAY DIFFRACTION12.26TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1573-2.22070.34181240.3007238194
2.2207-2.29240.35381340.27262550100
2.2924-2.37430.30681340.26492531100
2.3743-2.46940.29711330.26942524100
2.4694-2.58180.32131350.26752564100
2.5818-2.71790.30541350.24632558100
2.7179-2.88810.28961340.23262555100
2.8881-3.11110.25751360.23382568100
3.1111-3.42410.24731350.20642592100
3.4241-3.91930.19471380.17412610100
3.9193-4.93690.18471380.14012635100
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)
14.5979-5.4863-4.0976.52874.88493.6483-0.0169-0.0542-0.3092-0.3383-0.35050.6105-0.5161-0.56940.32370.47950.1310.00780.60320.03090.39933.019625.1174-7.9374
28.916-6.7658-7.47597.64127.53088.86240.20.09040.1897-0.559-0.0594-0.2426-0.50820.0458-0.15710.45270.0706-0.00910.44160.04640.268410.194728.9995-7.3741
32.20120.0311.2442.7977-2.18763.9779-0.08040.1407-0.044-0.2898-0.0253-0.19650.48260.32980.11650.52490.09510.07820.28470.0030.281915.721643.0472-49.3579
45.25270.9849-0.53593.7594-0.79393.6471-0.0503-0.04090.285-0.35840.03260.49050.0698-0.41470.03570.35270.0257-0.06160.36-0.02920.3081-3.327829.975-23.7946
55.1315-0.9314-1.87553.74593.97286.5996-0.21740.3022-0.27640.1457-0.25980.50790.2657-0.69380.43530.4339-0.00290.09130.3141-0.00520.3668-8.689655.1102-40.515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid 1 through 31)D1 - 31
2X-RAY DIFFRACTION2(chain 'E' and resid 1 through 31)E1 - 31
3X-RAY DIFFRACTION3(chain 'A' and resid 3 through 115)A3 - 115
4X-RAY DIFFRACTION4(chain 'B' and resid 2 through 117)B2 - 117
5X-RAY DIFFRACTION5(chain 'C' and resid 2 through 115)C2 - 115

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