9c6y

Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab

Method: X-RAY DIFFRACTION

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

;Spike protein S2' ;

Severe acute respiratory syndrome coronavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Heavy chain of COV2-3906 Fab × 1 Light chain of COV2-3906 Fab × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SULFATE ION × 4 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 water × 3	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 1	Heavy chain of COV2-3906 Fab × 1 Light chain of COV2-3906 Fab × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SULFATE ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 water × 3	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	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–216； UniProt 319–534 Author chain F； PDBConstruct 1–216； UniProt 319–534

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	9c6y
Deposition date deposition_date	2024-06-10
Structure title title	Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab
Keywords keywords	coronavirus, antibody, fab, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

9c6y__assembly_1__model_1

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

Download this curve (.dat)

9c6y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c6y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.56 Å
Rg (electron density)	32.32 Å
Total Rg	32.86 Å
Atom count	5037
Residues	650
Excluded volume	89009 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c6y__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9c6y__assembly_2__model_1`	trimeric （3）	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 (10)

Entity 1 Entity 1 polymer

Description description	Heavy chain of COV2-3906 Fab
Molecular weight formula_weight	23972.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	10096

QVQLQESGPGLVKPSQTLSLTCTVSGDSISSDGYYWSWLRQRPGKGLEWIGYIYNSGSTHYNPSLNSRVSISIDTSKTQFSLKLSSVTAADTAVYYCARALVLITYVWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Light chain of COV2-3906 Fab
Molecular weight formula_weight	23098.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

NFMLTQPHSVSESPGKTVTISCTGSSGSVASNYVQWYQHRPGSAPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISELKPEDEADYYCQSYGDRNVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	;Spike protein S2' ;
Molecular weight formula_weight	24446.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

RVQPTESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADFSVIYNFAPFFAFKCYGVSPTKLNDLCWTNIYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKLEVLFQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus
NCBI taxonomy ID ncbi_taxonomy_id	2901879
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	894.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

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 non-polymer

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

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

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Unit-cell length a length_a	66.971 Å
Unit-cell length b length_b	170.851 Å
Unit-cell length c length_c	231.543 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.680 Å
Low-resolution limit resolution_low	48.500 Å
R factor r_factor	0.2082
R_work r_work	0.2073
R_free r_free	0.2418

Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab

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

;Spike protein S2' ;

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

9c6y__assembly_1__model_1

9c6y__assembly_1__model_1 | I(q)

9c6y__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)

Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab

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

;Spike protein S2' ;

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

9c6y__assembly_1__model_1

9c6y__assembly_1__model_1 | I(q)

9c6y__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)