8bh5

SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody

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 4 其他Polymer 1	Beta-27 heavy chain × 1 Beta-27 light chain × 1 Nanobody C1 × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GLYCEROL × 12 PHOSPHATE ION × 1 water × 4	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 7–202； UniProt 333–528

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	8bh5
Deposition date deposition_date	2022-10-29
Structure title title	SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody
Keywords keywords	Viral Protein/Immune system, SARS-CoV-2, Omicron, BA.2.12.1, RBD, Beta-27, IMMUNE SYSTEM; 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.

8bh5__assembly_1__model_1

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

Download this curve (.dat)

8bh5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8bh5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.30 Å
Rg (electron density)	31.94 Å
Total Rg	32.60 Å
Atom count	5806
Residues	742
Excluded volume	102560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8bh5__assembly_1__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	Beta-27 heavy chain
Molecular weight formula_weight	23532.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	5982

EVQLLESGGGLVQPGGSLRLSCAASGLTVRSNYMNWVRQAPGKGLEWVSLIYSGGSTFYADSVKGRFTISRHDSKNTLYLQMNSLRAEDTAVYYCARDLVVYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Beta-27 light chain
Molecular weight formula_weight	23129.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPGTLSLSPGERATLSCRASQSVSSSSLAWYQQKHGQAPRLLIYGTSSRATGIPDRFSGSGSGTDFTLTISGLEPEDFAVYYCQQYGSSPLFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Spike protein S1
Molecular weight formula_weight	23045.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

HHHHHHTNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKK

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Nanobody C1
Molecular weight formula_weight	14659.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLVESGGGLVQPGGSLRLSCAASGFTNDFYSIAWFRQAPGKEREGVSWLSVSDNTPTYVDSVKDRFTISRHNANNTVYLQMNMLKPEDTAIYYCAAGRFAGRDTWPSSYDYWGQGTQVTVSSKHHHHHH

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 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	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	8bh5C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8bh5H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8bh5H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8bh5L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8bh5L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	186.846 Å
Unit-cell length b length_b	99.987 Å
Unit-cell length c length_c	56.486 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	54.780 Å
R factor r_factor	0.1880
R_work r_work	0.1857
R_free r_free	0.2325

SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody

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

8bh5__assembly_1__model_1

8bh5__assembly_1__model_1 | I(q)

8bh5__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 (8)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody

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

8bh5__assembly_1__model_1

8bh5__assembly_1__model_1 | I(q)

8bh5__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 (8)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)