SAXSdb — 9ml8

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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 3 其他Polymer 1	M8b-B1 heavy chain × 1 M8b-B1 light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 2 water × 3	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 1	M8b-B1 heavy chain × 1 M8b-B1 light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 water × 3	Consistent with protein count
3	Other combination	Heteromer	Protein 3 其他Polymer 1	M8b-B1 heavy chain × 1 M8b-B1 light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 2 water × 3	Consistent with protein count
4	Other combination	Heteromer	Protein 3 其他Polymer 1	M8b-B1 heavy chain × 1 M8b-B1 light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 2 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–206； UniProt 328–533 Author chain B； PDBConstruct 1–206； UniProt 328–533 Author chain C； PDBConstruct 1–206； UniProt 328–533 Author chain D； PDBConstruct 1–206； UniProt 328–533

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	9ml8
Deposition date deposition_date	2024-12-18
Last revision last_revision	2025-06-04
Structure title title	Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Keywords keywords	immune system, neutralizing antibody, 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.

9ml8__assembly_1__model_1

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

Download this curve (.dat)

9ml8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ml8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.46 Å
Rg (electron density)	31.28 Å
Total Rg	31.80 Å
Atom count	4910
Residues	636
Excluded volume	86933 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ml8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9ml8__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9ml8__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9ml8__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	Spike protein S1
Molecular weight formula_weight	24004.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20452

RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLHHHHHH

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	SARS-CoV-2, 2019-nCoV, COVID-19 virus
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	M8b-B1 heavy chain
Molecular weight formula_weight	24956.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,H,M,P

QSLEESGGDLVKPGASLTLTCTASGFSFSGSYYMCWVRQAPGKGLEWIACIYDGSYDGSSDNAYYASWAKGRFTISKTSSTTVTLQMTSLTAADTATYFCARGVYFYAGHFVIMRYFVLWGPGTLVTVSSGQPKAPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	M8b-B1 light chain
Molecular weight formula_weight	23367.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,L,N,Q

AQVLTQTPSSVSAAVGGTVSISCQSSQSVYSNYLSWYQQKPGQPPKLLIYDASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCQGSYYSSDWYPFGGGTEVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	755

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Unit-cell length a length_a	175.074 Å
Unit-cell length b length_b	173.441 Å
Unit-cell length c length_c	129.928 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	39.150 Å
R factor r_factor	0.2230
R_work r_work	0.2227
R_free r_free	0.2468

Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab

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

9ml8__assembly_1__model_1

9ml8__assembly_1__model_1 | I(q)

9ml8__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab

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

9ml8__assembly_1__model_1

9ml8__assembly_1__model_1 | I(q)

9ml8__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)