PDB-8f2j: Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV...

ID or keywords:

Entry

Database: PDB / ID: 8f2j

Title

Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain

Components

Spike protein S1
WRAIR-2134 Fab Heavy Chain
WRAIR-2134 Fab Light Chain

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / WRAIR-2134 / receptor binding domain / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN

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

Homo sapiens (human)

Severe acute respiratory syndrome coronavirus 2

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.16 Å

Authors

Sankhala, R.S. / Joyce, M.G.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.
Authors: Sankhala, R.S. / Dussupt, V. / Jensen, J. / Modjarrad, K. / Joyce, M.G.

History

Deposition	Nov 8, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8f2j.cif.gz	984.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8f2j.ent.gz	826.6 KB	Display	PDB format
PDBx/mmJSON format	8f2j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8f2j_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8f2j_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8f2j_validation.xml.gz	83.5 KB	Display
Data in CIF	8f2j_validation.cif.gz	111 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f2/8f2j ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f2j	HTTPS FTP

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Related structure data

Related structure data	5gguS 6b0wS 7n4jS S: Starting model for refinement
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) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: WRAIR-2134 Fab Heavy Chain

B: WRAIR-2134 Fab Light Chain

D: WRAIR-2134 Fab Heavy Chain

F: WRAIR-2134 Fab Light Chain

H: WRAIR-2134 Fab Heavy Chain

I: WRAIR-2134 Fab Heavy Chain

J: WRAIR-2134 Fab Light Chain

L: WRAIR-2134 Fab Light Chain

C: Spike protein S1

E: Spike protein S1

G: Spike protein S1

K: Spike protein S1

hetero molecules

286 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: WRAIR-2134 Fab Heavy Chain

B: WRAIR-2134 Fab Light Chain

C: Spike protein S1

hetero molecules

defined by author
Evidence: gel filtration, Migrated as expected molecular mass on SEC column.
71.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: WRAIR-2134 Fab Heavy Chain

F: WRAIR-2134 Fab Light Chain

G: Spike protein S1

hetero molecules

defined by author
71.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

H: WRAIR-2134 Fab Heavy Chain

L: WRAIR-2134 Fab Light Chain

E: Spike protein S1

hetero molecules

defined by author
71.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

I: WRAIR-2134 Fab Heavy Chain

J: WRAIR-2134 Fab Light Chain

K: Spike protein S1

hetero molecules

defined by author
71.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	143.190, 154.430, 165.250
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody

WRAIR-2134 Fab Heavy Chain

Mass: 25186.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Antibody Heavy Chain Fab fragment / Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#2: Antibody

WRAIR-2134 Fab Light Chain

Mass: 22809.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Antibody Light Chain / Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#3: Protein

Spike protein S1

Mass: 23073.766 Da / Num. of mol.: 4 / Fragment: receptor binding domain (RBD)
Source method: isolated from a genetically manipulated source
Details: Viral protein
Source: (gene. exp.)

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

Homo sapiens (human) / References: UniProt: P0DTC2

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#5: 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

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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: 3.21 Å³/Da / Density % sol: 61.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 3.15→50 Å / Num. obs: 121509 / % possible obs: 99.7 % / Redundancy: 3.57 % / CC_1/2: 0.99 / R_sym value: 0.149 / Net I/σ(I): 7.15
Reflection shell	Resolution: 3.15→3.33 Å / Mean I/σ(I) obs: 1.05 / Num. unique obs: 19496 / CC_1/2: 0.428 / R_sym value: 1.43 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GGU, 6B0W, 7N4J

5ggu

6b0w

7n4j

Resolution: 3.16→19.96 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2453	2974	5.07 %
R_work	0.2088	-	-
obs	0.2106	58671	92.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.16→19.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19573	0	84	0	19657

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004
X-RAY DIFFRACTION	f_angle_d	0.799
X-RAY DIFFRACTION	f_dihedral_angle_d	13.748	7165
X-RAY DIFFRACTION	f_chiral_restr	0.051	3019
X-RAY DIFFRACTION	f_plane_restr	0.005	3542

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 (%)
3.16-3.21	0.3606	25	0.2987	402	X-RAY DIFFRACTION
3.21-3.27	0.2502	84		1411	X-RAY DIFFRACTION	50
3.27-3.33	0.3295	139	0.3109	2419	X-RAY DIFFRACTION	87
3.33-3.39	0.367	141	0.3032	2845	X-RAY DIFFRACTION	100
3.39-3.46	0.3557	144	0.2802	2802	X-RAY DIFFRACTION	100
3.46-3.53	0.319	144	0.2662	2848	X-RAY DIFFRACTION	100
3.53-3.61	0.3128	133	0.2528	2838	X-RAY DIFFRACTION	100
3.61-3.7	0.2819	164	0.2542	2813	X-RAY DIFFRACTION	100
3.7-3.8	0.3083	144	0.2424	2829	X-RAY DIFFRACTION	100
3.8-3.91	0.2397	163	0.2302	2825	X-RAY DIFFRACTION	100
3.91-4.04	0.2365	161	0.2124	2851	X-RAY DIFFRACTION	100
4.04-4.18	0.2272	141	0.1999	2830	X-RAY DIFFRACTION	100
4.18-4.35	0.205	161	0.1791	2853	X-RAY DIFFRACTION	100
4.35-4.54	0.2286	164	0.1716	2809	X-RAY DIFFRACTION	100
4.54-4.78	0.184	124	0.1716	2909	X-RAY DIFFRACTION	100
4.78-5.08	0.2178	158	0.1768	2848	X-RAY DIFFRACTION	100
5.08-5.46	0.212	149	0.1825	2868	X-RAY DIFFRACTION	100
5.46-6	0.2356	168	0.2062	2865	X-RAY DIFFRACTION	100
6-6.83	0.2337	153	0.2158	2905	X-RAY DIFFRACTION	100
6.84-8.5	0.2679	160	0.1941	2917	X-RAY DIFFRACTION	100
8.5-19.96	0.2027	154	0.1734	3010	X-RAY DIFFRACTION	99

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	2.3947	1.5542	-0.4528	2.711	-0.1568	1.101	-0.203	-0.1093	0.389	-0.13	0.1628	0.0123	-0.0912	-0.0668	0	0.5393	0.1521	-0.1498	0.4408	-0.0636	0.6917	5.33	-39.327	13.358
2	1.8041	1.6524	-0.1634	3.1172	-0.3938	1.2467	0.2936	-0.4777	0.1604	0.7978	-0.2634	-0.1036	-0.1647	0.0519	0.0111	0.8946	0.0759	-0.1242	0.7008	-0.1411	0.6351	11.468	-41.258	29.809
3	1.5236	-0.0078	-0.0962	1.8159	0.8063	1.0129	-0.0638	-0.3162	0.075	0.0056	0.0097	-0.2638	-0.0077	0.2072	0.0275	0.4774	-0.0105	-0.107	0.5141	0.0646	0.4714	-24.407	3.406	16.781
4	1.6424	-0.3873	-0.3713	2.5485	-0.0473	0.6116	-0.0717	-0.229	-0.0691	0.1401	-0.0499	-0.0092	0.0286	0.0766	0.0749	0.4837	0.0258	-0.1342	0.4401	0.0434	0.3598	-38.3	-1.879	24.317
5	2.0131	-1.351	-0.2194	2.634	0.727	0.7998	-0.1325	0.1633	-0.1087	-0.0334	0.0236	0.1546	0.1339	-0.0044	0.0605	0.5186	-0.0755	0.0386	0.3976	0.0233	0.4142	-37.438	-38.077	67.897
6	1.6944	-0.7216	0.5951	3.0113	-1.0801	0.9014	0.0966	-0.2653	-0.2876	0.0078	-0.0067	0.5375	0.0354	-0.1937	-0.0067	0.4828	0.0239	0.0812	0.5498	-0.0384	0.5407	-78.761	-1.918	14.91
7	1.6127	-0.4205	0.3489	2.612	-0.7059	0.8351	-0.1355	-0.1532	-0.2061	0.2462	0.092	0.1964	-0.0147	-0.1155	0.0342	0.4459	0.0477	0.0554	0.4859	0.0012	0.4478	-65.319	3.842	22.863
8	1.2071	-1.259	0.0784	2.7383	0.119	1.1123	0.1339	0.6566	-0.0192	-0.505	-0.2207	0.0663	0.191	-0.2052	0.0432	0.6812	-0.0674	0.0096	0.6698	0.1032	0.4309	-33.832	-35.876	50.684
9	3.3623	1.269	0.6857	2.7816	0.2439	2.0705	0.2827	-0.3061	-0.862	1.3261	-0.0714	0.4864	0.3616	-0.2413	-0.123	1.0828	-0.0998	0.108	0.6022	0.0278	0.9067	-20.858	-77.282	21.106
10	2.6777	-2.1602	0.1572	4.2186	0.0272	1.7606	-0.1232	0.3607	1.1153	0.3557	0.0429	0.0541	-0.5894	-0.2994	-0.0602	0.786	0.1334	-0.1588	0.4556	0.194	1.114	-63.781	0.795	65.721
11	2.2014	0.4628	1.0671	3.7269	0.8244	3.4268	-0.2802	0.1468	-0.096	-0.1788	0.297	0.2056	-0.2111	0.1637	-0.0345	0.558	0.0026	0.1009	0.3742	0.0462	0.8262	-30.163	-39.925	-2.598
12	2.1742	0.6717	-0.6561	2.7879	0.2413	2.885	-0.2	0.1139	0.0885	-0.3871	0.1367	-0.0017	0.0745	-0.1095	0.0276	0.4241	0.0752	-0.1094	0.4148	-0.0077	0.561	-70.171	39.909	-7.947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:229 )	A	1 - 229
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 10:220 )	B	10 - 220
3	X-RAY DIFFRACTION	3	( CHAIN D AND RESID 1:231 )	D	1 - 231
4	X-RAY DIFFRACTION	4	( CHAIN F AND RESID 10:220 )	F	10 - 220
5	X-RAY DIFFRACTION	5	( CHAIN H AND RESID 1:231 )	H	1 - 231
6	X-RAY DIFFRACTION	6	( CHAIN I AND RESID 1:230 )	I	1 - 230
7	X-RAY DIFFRACTION	7	( CHAIN J AND RESID 9:220 )	J	9 - 220
8	X-RAY DIFFRACTION	8	( CHAIN L AND RESID 10:220 )	L	10 - 220
9	X-RAY DIFFRACTION	9	( CHAIN C AND ( RESID 334:532 OR RESID 601:601 ) )	C	334 - 532
10	X-RAY DIFFRACTION	9	( CHAIN C AND ( RESID 334:532 OR RESID 601:601 ) )	C	601
11	X-RAY DIFFRACTION	10	( CHAIN E AND ( RESID 334:531 OR RESID 601:601 ) )	E	334 - 531
12	X-RAY DIFFRACTION	10	( CHAIN E AND ( RESID 334:531 OR RESID 601:601 ) )	E	601
13	X-RAY DIFFRACTION	11	( CHAIN G AND RESID 334:529 )	G	334 - 529
14	X-RAY DIFFRACTION	12	( CHAIN K AND RESID 333:529 )	K	333 - 529

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