7wqv

Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S1

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Ab08 × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 CALCIUM ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ab08 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CALCIUM ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 1	Consistent with protein count
3	Other combination	Heteromer	Protein 2 其他Polymer 1	Ab08 × 1 alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
4	Other combination	Heteromer	Protein 2 其他Polymer 1	Ab08 × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CHLORIDE ION × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Ab08 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 4	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Ab08 × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Ab08 × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Ab08 × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CALCIUM ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–226； UniProt 330–531 Author chain C； PDBConstruct 25–226； UniProt 330–531 Author chain E； PDBConstruct 25–226； UniProt 330–531 Author chain G； PDBConstruct 25–226； UniProt 330–531 Author chain I； PDBConstruct 25–226； UniProt 330–531 Author chain K； PDBConstruct 25–226； UniProt 330–531 Author chain M； PDBConstruct 25–226； UniProt 330–531 Author chain O； PDBConstruct 25–226； UniProt 330–531

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7wqv
Deposition date deposition_date	2022-01-26
Structure title title	Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)
Keywords keywords	;Ab08, mAb, Coronavirus, Covid-19, Monoclonal antibody, nAb, Neutralizing antibody, RBD, Receptor-binding domain, SARS-CoV-2, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7wqv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7wqv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7wqv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.45 Å
Rg (electron density)	22.54 Å
Total Rg	23.58 Å
Atom count	3363
Residues	437
Excluded volume	59460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7wqv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7wqv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7wqv__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7wqv__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`7wqv__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`7wqv__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`7wqv__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`7wqv__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Spike protein S1
Molecular weight formula_weight	26214.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	26586

MKFLVNVALVFMVVYISYIYAAGSPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTGTLEVLFQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Ab08
Molecular weight formula_weight	31367.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P

MSKYLLPTAAAGLLLLAAQPAMAGSSSQVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGIIPILGTTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARKFGYSGYGATWYFDLWGRGTLVTVSSGGGGSGGGGSGGGGSQSVLTQPPSVSGAPGQRVTISCTGNSSNIGAGYDVHWYQQFPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLAGRAGEQKLISEEDLNSAVDHHHHHH

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli MC1061

Entity 3 Entity 3 branched

Description description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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Unit-cell length a length_a	92.643 Å
Unit-cell length b length_b	116.742 Å
Unit-cell length c length_c	180.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	44.930 Å
R factor r_factor	0.2213
R_work r_work	0.2198
R_free r_free	0.2510

Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7wqv__assembly_1__model_1

7wqv__assembly_1__model_1 | I(q)

7wqv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike protein S1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7wqv__assembly_1__model_1

7wqv__assembly_1__model_1 | I(q)

7wqv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)