PDB-8opi: VHH Z70 mutant 1 in interaction with PHF6 Tau peptide

ID or keywords:

Entry

Database: PDB / ID: 8opi

Title

VHH Z70 mutant 1 in interaction with PHF6 Tau peptide

Components

PHF6 Tau peptide
VHH Z70 mutant 1

Keywords

IMMUNE SYSTEM / VHH / nanobody / complex

Biological species

Lama glama (llama)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Dupre, E. / Mortelecque, J. / NGuyen, M. / Hanoulle, X. / Landrieu, I.

Funding support

France, 2items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: A selection and optimization strategy for single-domain antibodies targeting the PHF6 linear peptide within the tau intrinsically disordered protein.
Authors: Mortelecque, J. / Zejneli, O. / Begard, S. / Simoes, M.C. / ElHajjar, L. / Nguyen, M. / Cantrelle, F.X. / Hanoulle, X. / Rain, J.C. / Colin, M. / Gomes, C.M. / Buee, L. / Landrieu, I. / Danis, C. / Dupre, E.

History

Deposition	Apr 7, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 24, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8opi.cif.gz	63 KB	Display	PDBx/mmCIF format
PDB format	pdb8opi.ent.gz	44.2 KB	Display	PDB format
PDBx/mmJSON format	8opi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8opi_validation.pdf.gz	434.3 KB	Display	wwPDB validaton report
Full document	8opi_full_validation.pdf.gz	434.9 KB	Display
Data in XML	8opi_validation.xml.gz	7.8 KB	Display
Data in CIF	8opi_validation.cif.gz	10.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/8opi ftp://data.pdbj.org/pub/pdb/validation_reports/op/8opi	HTTPS FTP

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Related structure data

Related structure data	8op0C 8piiC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: VHH Z70 mutant 1

B: PHF6 Tau peptide

15.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: surface plasmon resonance

Unit cell

Length a, b, c (Å)	135.165, 135.165, 35.411
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Antibody	VHH Z70 mutant 1 Mass: 13844.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein/peptide	PHF6 Tau peptide Mass: 1460.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.68 % / Description: Hexagonal rod
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1.7M Ammonium Sulfate, 4.25% Isopropanol, 15% lLycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.978565 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978565 Å / Relative weight: 1

Reflection

Resolution: 1.83→44.24 Å / Num. obs: 17371 / % possible obs: 100 % / Redundancy: 39.5 % / CC_1/2: 1 / R_merge(I) obs: 0.155 / R_pim(I) all: 0.034 / R_rim(I) all: 0.159 / Net I/σ(I): 20

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.97-44.24	30.3	0.045	17371	0.999	0.01	0.046
1.83-1.87	39.3	3.123	191	0.902	0.7	3.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
REFMAC	5.8.0405	refinement
Coot		model building
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.83→44.24 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.942 / SU B: 2.436 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2301	866	4.99 %
R_work	0.1976	16489	-
all	0.199	-	-
obs	-	17355	99.948 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 30.698 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.002 Å²	0.501 Å²	0 Å²
2-	-	1.002 Å²	0 Å²
3-	-	-	-3.251 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→44.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	919	0	0	89	1008

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.011	959
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	857
X-RAY DIFFRACTION	r_angle_refined_deg	1.827	1.644	1302
X-RAY DIFFRACTION	r_angle_other_deg	0.61	1.562	1973
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.902	5	130
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.848	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.461	10	145
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.714	10	40
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	141
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1157
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	239
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	140
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	759
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	480
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	544
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	66
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.175	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.166	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	4.195	3.208	499
X-RAY DIFFRACTION	r_mcbond_other	4.196	3.207	499
X-RAY DIFFRACTION	r_mcangle_it	5.781	5.694	621
X-RAY DIFFRACTION	r_mcangle_other	5.779	5.698	622
X-RAY DIFFRACTION	r_scbond_it	4.924	3.518	460
X-RAY DIFFRACTION	r_scbond_other	4.919	3.522	461
X-RAY DIFFRACTION	r_scangle_it	7.249	6.224	676
X-RAY DIFFRACTION	r_scangle_other	7.246	6.227	677
X-RAY DIFFRACTION	r_lrange_it	9.538	34.286	1076
X-RAY DIFFRACTION	r_lrange_other	9.488	33.77	1056

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.83-1.877	0.304	60	0.289	1188	X-RAY DIFFRACTION	99.9199
1.877-1.929	0.237	61	0.247	1149	X-RAY DIFFRACTION	100
1.929-1.985	0.217	60	0.232	1142	X-RAY DIFFRACTION	100
1.985-2.046	0.212	58	0.194	1089	X-RAY DIFFRACTION	100
2.046-2.112	0.251	56	0.198	1074	X-RAY DIFFRACTION	100
2.112-2.186	0.197	54	0.18	1029	X-RAY DIFFRACTION	100
2.186-2.269	0.199	52	0.179	991	X-RAY DIFFRACTION	100
2.269-2.361	0.266	51	0.2	981	X-RAY DIFFRACTION	100
2.361-2.466	0.266	49	0.193	912	X-RAY DIFFRACTION	100
2.466-2.586	0.202	47	0.183	893	X-RAY DIFFRACTION	100
2.586-2.725	0.241	45	0.186	865	X-RAY DIFFRACTION	100
2.725-2.89	0.218	42	0.193	791	X-RAY DIFFRACTION	100
2.89-3.088	0.283	40	0.209	760	X-RAY DIFFRACTION	100
3.088-3.334	0.252	37	0.194	716	X-RAY DIFFRACTION	100
3.334-3.651	0.208	36	0.168	667	X-RAY DIFFRACTION	100
3.651-4.078	0.161	31	0.175	605	X-RAY DIFFRACTION	100
4.078-4.702	0.174	29	0.154	537	X-RAY DIFFRACTION	100
4.702-5.743	0.309	25	0.208	474	X-RAY DIFFRACTION	100
5.743-8.054	0.29	20	0.284	378	X-RAY DIFFRACTION	100
8.054-44.24	0.272	13	0.274	248	X-RAY DIFFRACTION	100

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