PDB-6zbp: H11-H4 complex with SARS-CoV-2

ID or keywords:

Entry

Database: PDB / ID: 6zbp

Title

H11-H4 complex with SARS-CoV-2

Components

H11-H4
Spike glycoproteinSpike protein

Keywords

ANTIVIRAL PROTEIN /

Complex /

llama /

nanobody /

antibody /

SARS-CoV-2

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: 1.85 Å

Authors

Naismith, J.H. / Huo, J. / Mikolajek, H. / Ward, P. / Dumoux, M. / Owens, R.J. / LeBas, A.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: H11-D4 complex with SARS-CoV-2 RBD
Authors: Naismith, J.H.

History

Deposition	Jun 8, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6zbp.cif.gz	246.3 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	6zbp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/6zbp ftp://data.pdbj.org/pub/pdb/validation_reports/zb/6zbp	HTTPS FTP

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Related structure data

Related structure data	6yz5SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6yz5-d 11978 4kzg-7 2wqv-2 5h28-d 1xmx-d 4ckt-d 6f5g-d 4kzg-6 2wqv-1 Search similar-shape structures by Omokage search (details) 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) #21 - Sep 2001 Antibodies similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

EEE: Spike glycoprotein

FFF: H11-H4

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.150, 73.150, 131.670
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	EEE-763- HOH

#1: Protein

Spike glycoprotein /

Spike protein / S glycoprotein / E2 / Peplomer protein

Mass: 23716.580 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

H11-H4

Mass: 15045.752 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: isolated from a genetically manipulated source
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

#4: Chemical

ChemComp-SO4 / SULFATE ION /

Sulfate

Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O

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: 2.62 Å³/Da / Density % sol: 53.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium ...Details: Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.

Crystal

Density Matthews: 2.62 Å³/Da / Density % sol: 53.12 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium ...

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: liquid N2 / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97623 Å / Relative weight: 1
Reflection	Resolution: 1.85→57.151 Å / Num. obs: 35506 / % possible obs: 99.5 % / Redundancy: 19.7 % / CC_1/2: 1 / R_merge(I) obs: 0.086 / R_pim(I) all: 0.028 / Net I/σ(I): 18.2
Reflection shell	Resolution: 1.85→1.9 Å / Redundancy: 20.9 % / R_merge(I) obs: 2.05 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2585 / CC_1/2: 0.7 / R_pim(I) all: 0.46 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XSCALE		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YZ5

6yz5

Resolution: 1.85→57.151 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.954 / SU B: 7.218 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2169	1808	5.097 %
R_work	0.185	33664	-
all	0.187	-	-
obs	-	35472	99.733 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.736 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.091 Å²	1.046 Å²	0 Å²
2-	-	2.091 Å²	-0 Å²
3-	-	-	-6.784 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→57.151 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2546	0	19	103	2668

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2696
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2350
X-RAY DIFFRACTION	r_angle_refined_deg	1.682	1.656	3680
X-RAY DIFFRACTION	r_angle_other_deg	1.405	1.58	5454
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	17.387	5.303	347
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.74	21.69	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.462	15	404
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	24.12	15	2
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.664	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	338
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3306
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	640
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	380
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2081
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1283
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1265
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	91
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.146	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.233	0.2	11
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.082	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.014	2.519	1314
X-RAY DIFFRACTION	r_mcbond_other	3.006	2.516	1313
X-RAY DIFFRACTION	r_mcangle_it	3.896	3.761	1646
X-RAY DIFFRACTION	r_mcangle_other	3.895	3.765	1647
X-RAY DIFFRACTION	r_scbond_it	4.612	3.06	1382
X-RAY DIFFRACTION	r_scbond_other	4.553	3.052	1379
X-RAY DIFFRACTION	r_scangle_it	6.874	4.396	2027
X-RAY DIFFRACTION	r_scangle_other	6.777	4.381	2022
X-RAY DIFFRACTION	r_lrange_it	8.797	29.077	2861
X-RAY DIFFRACTION	r_lrange_other	8.808	28.929	2851

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 (%)
1.85-1.898	0.333	125	0.3	2460	X-RAY DIFFRACTION	99.4231
1.898-1.95	0.277	135	0.272	2377	X-RAY DIFFRACTION	99.2493
1.95-2.006	0.258	136	0.233	2306	X-RAY DIFFRACTION	99.511
2.006-2.068	0.248	123	0.21	2248	X-RAY DIFFRACTION	99.6218
2.068-2.136	0.233	130	0.196	2166	X-RAY DIFFRACTION	99.6528
2.136-2.211	0.188	109	0.192	2148	X-RAY DIFFRACTION	99.6908
2.211-2.294	0.225	107	0.177	2053	X-RAY DIFFRACTION	99.9075
2.294-2.388	0.212	111	0.172	1960	X-RAY DIFFRACTION	99.8072
2.388-2.494	0.236	73	0.173	1926	X-RAY DIFFRACTION	99.8003
2.494-2.615	0.243	104	0.195	1841	X-RAY DIFFRACTION	99.8973
2.615-2.756	0.207	129	0.206	1691	X-RAY DIFFRACTION	99.9451
2.756-2.923	0.212	78	0.194	1664	X-RAY DIFFRACTION	99.8281
2.923-3.125	0.223	74	0.198	1560	X-RAY DIFFRACTION	99.8778
3.125-3.374	0.226	86	0.178	1435	X-RAY DIFFRACTION	99.8687
3.374-3.695	0.234	70	0.185	1356	X-RAY DIFFRACTION	100
3.695-4.13	0.208	69	0.166	1223	X-RAY DIFFRACTION	100
4.13-4.765	0.157	36	0.142	1107	X-RAY DIFFRACTION	99.9126
4.765-5.828	0.171	55	0.169	937	X-RAY DIFFRACTION	99.8993
5.828-8.207	0.243	34	0.197	756	X-RAY DIFFRACTION	100
8.207-57.151	0.255	24	0.221	450	X-RAY DIFFRACTION	99.3711

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	2.5606	-0.4707	0.9316	1.258	-0.4326	3.8177	0.1069	0.0558	-0.2388	0.0292	-0.1307	-0.4566	0.5136	0.5094	0.0238	0.163	0.0535	-0.0221	0.1136	0.0008	0.5533	32.463	-0.342	-8.231
2	2.3523	-0.3272	0.1284	3.9846	-0.4168	3.0845	0.0138	-0.1013	-0.1228	0.2361	0.0284	0.1443	0.2202	-0.1345	-0.0422	0.1163	-0.0155	-0.0271	0.0108	0.0228	0.3363	22.43	2.08	-7.989
3	2.1007	-0.8653	2.0231	2.7011	-1.5163	3.9669	0.0566	0.0398	-0.0184	0.0742	0.0313	0.1065	-0.0486	-0.0898	-0.0879	0.0369	0.0137	0.0448	0.0107	-0.0004	0.3513	17.757	10.896	-14.166
4	9.0909	0.7373	-5.0952	6.2173	1.2884	7.6775	-0.0084	1.0655	0.1477	-0.4062	0.0862	0.7049	-0.1427	-0.9554	-0.0777	0.1365	0.0677	0.0088	0.1951	0.0864	0.5116	5.969	24.838	-26.58
5	1.4569	-0.5379	0.7988	1.9709	-0.4844	3.4643	-0.0512	0.0221	-0.0177	0.5467	0.0427	-0.2737	0.0484	0.1856	0.0085	0.1734	0.0166	-0.0395	0.0249	0.0005	0.4177	25.972	5.787	-9.96
6	1.6596	0.1038	-0.5454	3.2321	-0.6823	2.5488	0.1427	-0.0138	0.1451	0.4101	-0.151	-0.2293	-0.4317	0.0791	0.0083	0.1329	-0.0069	0.0014	0.029	0.0332	0.4167	22.899	38.325	-27.586
7	4.2503	-3.7509	1.0647	9.6934	-1.5301	4.31	0.1348	0.1012	0.0269	-0.1012	-0.163	0.1411	-0.1626	-0.2529	0.0282	0.0429	0.0259	0.0259	0.0915	0.0227	0.3381	19.463	37.762	-34.082
8	1.4474	1.1916	-0.8304	5.1929	-1.6301	1.7619	0.1433	0.0167	0.1004	0.7147	-0.1484	0.0523	-0.6497	0.0484	0.0051	0.3294	-0.0148	-0.0099	0.0189	0.0146	0.4264	21.378	39.426	-23.651

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	EEE	334 - 387
2	X-RAY DIFFRACTION	2	ALL	EEE	388 - 417
3	X-RAY DIFFRACTION	3	ALL	EEE	418 - 479
4	X-RAY DIFFRACTION	4	ALL	EEE	480 - 488
5	X-RAY DIFFRACTION	5	ALL	EEE	489 - 528
6	X-RAY DIFFRACTION	6	ALL	FFF	1 - 64
7	X-RAY DIFFRACTION	7	ALL	FFF	65 - 88
8	X-RAY DIFFRACTION	8	ALL	FFF	89 - 128

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