PDB-8oww: B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)

ID or keywords:

Entry

Database: PDB / ID: 8oww

Title

B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)

Components

B5-5 nanobody
Spike protein S2'

Keywords

VIRAL PROTEIN /

Nanobody /

SARS-CoV-2 /

receptor binding domain /

complex

Function / homology

Function and homology information

Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.969 Å

Authors

Cornish, K.A.S. / Naismith, J.H. / Owens, R.J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)
Authors: Cornish, K.A.S. / Naismith, J.H. / Owens, R.J.

History

Deposition	Apr 28, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8oww.cif.gz	328.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8oww.ent.gz	207.2 KB	Display	PDB format
PDBx/mmJSON format	8oww.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/8oww ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8oww	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (2) #264 - Dec 2021 SARS-CoV-2 Spike Variants similarity (1) #246 - Jun 2020 SARS-CoV-2 Spike similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: Spike protein S2'

B: B5-5 nanobody

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	45.038, 70.029, 109.005
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	B-326- HOH
2	1	B-333- HOH

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Protein / Antibody / Sugars , 3 types, 3 molecules AB

#1: Protein

Spike protein S2'

Mass: 22644.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host:

Homo sapiens (human) / References: UniProt: P0DTC2

#2: Antibody

B5-5 nanobody

Mass: 13591.973 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)

#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 /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 107 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Tris pH 8.5, PEG smear low Seeded from crystals grown in ammonium nitrate, PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 1.969→45.079 Å / Num. obs: 25155 / % possible obs: 99.9 % / Redundancy: 53.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.2 / R_pim(I) all: 0.038 / R_rim(I) all: 0.203 / Net I/σ(I): 15.3

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
9.02-45.04	45.9	0.069	319	0.999	0.013	0.07
1.97-2.02	55.5	7.33	1708	0.461	1.373	7.458

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
xia2.multiplex		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building
PARROT		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.969→45.079 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.96 / SU B: 11.128 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2231	1264	5.033 %
R_work	0.1806	23849	-
all	0.183	-	-
obs	-	25113	99.861 %

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: 51.534 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.966 Å²	0 Å²	-0 Å²
2-	-	-1.465 Å²	-0 Å²
3-	-	-	-0.501 Å²

Refinement step

Cycle: LAST / Resolution: 1.969→45.079 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2496	0	46	100	2642

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.011	2605
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	2327
X-RAY DIFFRACTION	r_angle_refined_deg	2.182	1.653	3537
X-RAY DIFFRACTION	r_angle_other_deg	0.684	1.563	5335
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.695	5	319
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.156	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.112	10	371
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.409	10	125
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	377
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3126
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	667
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	428
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	2221
X-RAY DIFFRACTION	r_nbtor_refined	0.197	0.2	1289
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.095	0.2	1527
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.223	0.2	98
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.17	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.29	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.463	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	4.283	3.345	1282
X-RAY DIFFRACTION	r_mcbond_other	4.282	3.344	1282
X-RAY DIFFRACTION	r_mcangle_it	5.823	5.988	1599
X-RAY DIFFRACTION	r_mcangle_other	5.822	5.988	1600
X-RAY DIFFRACTION	r_scbond_it	5.513	3.868	1323
X-RAY DIFFRACTION	r_scbond_other	5.511	3.871	1324
X-RAY DIFFRACTION	r_scangle_it	7.684	6.828	1938
X-RAY DIFFRACTION	r_scangle_other	7.682	6.83	1939
X-RAY DIFFRACTION	r_lrange_it	9.923	35.817	2810
X-RAY DIFFRACTION	r_lrange_other	9.921	35.826	2811

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.969-2.02	0.338	90	0.334	1708	0.334	1818	0.9	0.902	98.8999	0.337
2.02-2.075	0.337	78	0.299	1704	0.3	1784	0.906	0.929	99.8879	0.296
2.075-2.135	0.29	79	0.266	1648	0.267	1731	0.939	0.945	99.7689	0.261
2.135-2.201	0.27	98	0.237	1572	0.239	1674	0.945	0.96	99.761	0.228
2.201-2.273	0.27	81	0.224	1557	0.226	1640	0.935	0.964	99.8781	0.205
2.273-2.352	0.23	89	0.202	1478	0.203	1567	0.963	0.973	100	0.178
2.352-2.441	0.226	82	0.183	1445	0.185	1528	0.963	0.979	99.9346	0.159
2.441-2.54	0.229	72	0.186	1420	0.188	1492	0.966	0.979	100	0.161
2.54-2.653	0.256	71	0.178	1347	0.182	1418	0.973	0.981	100	0.15
2.653-2.782	0.24	71	0.179	1291	0.182	1362	0.962	0.981	100	0.152
2.782-2.932	0.237	71	0.177	1211	0.181	1282	0.964	0.98	100	0.154
2.932-3.109	0.213	64	0.171	1168	0.173	1232	0.972	0.983	100	0.152
3.109-3.322	0.256	50	0.179	1112	0.182	1162	0.959	0.981	100	0.165
3.322-3.587	0.228	56	0.169	1036	0.172	1092	0.967	0.983	100	0.164
3.587-3.927	0.229	44	0.157	959	0.16	1003	0.97	0.985	100	0.158
3.927-4.386	0.19	46	0.15	877	0.152	923	0.982	0.988	100	0.156
4.386-5.057	0.192	48	0.124	769	0.127	817	0.977	0.991	100	0.14
5.057-6.174	0.206	35	0.179	668	0.18	703	0.977	0.984	100	0.197
6.174-8.65	0.187	26	0.199	537	0.198	563	0.984	0.975	100	0.224
8.65-45.079	0.187	13	0.218	342	0.217	355	0.99	0.961	100	0.24

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.5201	-0.5935	-1.122	2.0857	0.5136	2.5099	0.0031	-0.5576	-0.1812	0.1882	0.0179	-0.0198	0.1947	0.2225	-0.021	0.0522	-0.0457	-0.0156	0.1774	0.0389	0.0142	13.1693	4.2858	21.6207
2	1.4788	-0.3617	-0.0502	5.4489	-1.0082	1.8017	0.1166	0.0633	0.2587	-0.0342	-0.1269	-0.0192	-0.2933	-0.104	0.0103	0.1086	-0.0126	0.0281	0.1377	0.016	0.089	9.4984	24.1469	7.1654

Refinement TLS group

Selection: ALL

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